Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	K	T	V	S	T	S	K	K	P	R	K	Q	H	S	P	E	F	R	S	E	A	L	K	L	A	E	R	I	G	V	T	A	A	A	R	E	L	S	L	Y	E	S	Q	L	Y	N	W	R	S	K	Q	Q	N	Q	Q	T	S	S
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?																																					?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.
Sequence		E	R	E	L	E	M	S	T	E	I	A	R	L	K	R	Q	L	A	E	R	D	E	E	L	A	I	L	Q	K	A	A	T	Y	F	A	K	R	L	K
Secondary structure
SS confidence
Disorder		?	?	?	?	?																																?	?	?
Disorder confidence

Confidence Key
High(9)											Low (0)

?	Disordered
	Alpha helix
	Beta strand

Domain analysis

Hover over an aligned region to see model and summary info

Please note, only up to the top 20 hits are modelled to reduce computer load

Rank Aligned region

PDB 2rn7 chain A Region: 9 - 97 Aligned: 89 Modelled: 89 Confidence: 99.8% Identity: 19% PDB header:unknown function Chain: A: PDB Molecule:is629 orfa; PDBTitle: nmr solution structure of tnpe protein from shigella2 flexneri. northeast structural genomics target sfr125 Phyre2 PDB 2jn6 chain A domain 1 Region: 10 - 97 Aligned: 85 Modelled: 88 Confidence: 99.8% Identity: 21% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Cgl2762-like Phyre2 PDB 2elh chain A Region: 2 - 52 Aligned: 51 Modelled: 51 Confidence: 98.3% Identity: 20% PDB header:dna binding protein Chain: A: PDB Molecule:cg11849-pa; PDBTitle: solution structure of the cenp-b n-terminal dna-binding2 domain of fruit fly distal antenna cg11849-pa Phyre2 PDB 1hlv chain A Region: 8 - 98 Aligned: 91 Modelled: 91 Confidence: 98.2% Identity: 15% PDB header:dna binding protein/dna Chain: A: PDB Molecule:major centromere autoantigen b; PDBTitle: crystal structure of cenp-b(1-129) complexed with the cenp-2 b box dna Phyre2 PDB 1pdn chain C Region: 13 - 63 Aligned: 51 Modelled: 51 Confidence: 98.1% Identity: 12% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Paired domain Phyre2 PDB 6pax chain A Region: 13 - 63 Aligned: 51 Modelled: 51 Confidence: 98.0% Identity: 12% PDB header:gene regulation/dna Chain: A: PDB Molecule:homeobox protein pax-6; PDBTitle: crystal structure of the human pax-6 paired domain-dna2 complex reveals a general model for pax protein-dna3 interactions Phyre2 PDB 6pax chain A domain 1 Region: 13 - 63 Aligned: 51 Modelled: 51 Confidence: 98.0% Identity: 12% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Paired domain Phyre2 PDB 1k78 chain A domain 1 Region: 13 - 61 Aligned: 49 Modelled: 49 Confidence: 98.0% Identity: 10% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Paired domain Phyre2 PDB 1u78 chain A Region: 10 - 65 Aligned: 56 Modelled: 56 Confidence: 97.9% Identity: 11% PDB header:dna binding protein/dna Chain: A: PDB Molecule:transposable element tc3 transposase; PDBTitle: structure of the bipartite dna-binding domain of tc32 transposase bound to transposon dna Phyre2 PDB 1hlv chain A domain 1 Region: 8 - 52 Aligned: 45 Modelled: 45 Confidence: 97.9% Identity: 18% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Centromere-binding Phyre2 PDB 1bw6 chain A Region: 8 - 51 Aligned: 44 Modelled: 44 Confidence: 97.8% Identity: 18% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Centromere-binding Phyre2 PDB 3hef chain B Region: 12 - 93 Aligned: 71 Modelled: 82 Confidence: 97.4% Identity: 13% PDB header:viral protein Chain: B: PDB Molecule:gene 1 protein; PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit Phyre2 PDB 2glo chain A Region: 11 - 55 Aligned: 45 Modelled: 45 Confidence: 97.3% Identity: 22% PDB header:transcription/dna Chain: A: PDB Molecule:brinker cg9653-pa; PDBTitle: solution structure of the brinker dna binding domain in2 complex with the omb enhancer Phyre2 PDB 2cob chain A domain 1 Region: 9 - 66 Aligned: 58 Modelled: 58 Confidence: 97.1% Identity: 14% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Psq domain Phyre2 PDB 2k27 chain A Region: 13 - 63 Aligned: 51 Modelled: 51 Confidence: 96.6% Identity: 10% PDB header:transcription regulator Chain: A: PDB Molecule:paired box protein pax-8; PDBTitle: solution structure of human pax8 paired box domain Phyre2 PDB 2w48 chain D Region: 16 - 79 Aligned: 64 Modelled: 64 Confidence: 96.2% Identity: 17% PDB header:transcription Chain: D: PDB Molecule:sorbitol operon regulator; PDBTitle: crystal structure of the full-length sorbitol operon2 regulator sorc from klebsiella pneumoniae Phyre2 PDB 2ao9 chain A domain 1 Region: 14 - 52 Aligned: 39 Modelled: 39 Confidence: 96.1% Identity: 31% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Nanomeric phage protein-like Phyre2 PDB 2r0q chain F Region: 17 - 54 Aligned: 38 Modelled: 38 Confidence: 95.4% Identity: 11% PDB header:recombination/dna Chain: F: PDB Molecule:putative transposon tn552 dna-invertase bin3; PDBTitle: crystal structure of a serine recombinase- dna regulatory2 complex Phyre2 PDB 1ntc chain A Region: 17 - 54 Aligned: 38 Modelled: 38 Confidence: 95.3% Identity: 24% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1fip chain A Region: 17 - 54 Aligned: 38 Modelled: 38 Confidence: 95.2% Identity: 21% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 1 c2rn7A_ 2 d2jn6a1 3 c2elhA_ 4 c1hlvA_ 5 d1pdnc_ 6 c6paxA_ 7 d6paxa1 8 d1k78a1 9 c1u78A_ 10 d1hlva1 11 d1bw6a_ 12 c3hefB_ 13 c2gloA_ 14 d2coba1 15 c2k27A_ 16 c2w48D_ 17 d2ao9a1 18 c2r0qF_ 19 d1ntca_ 20 d1fipa_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499

Detailed template information

# Template Alignment Coverage 3D Model Confidence % i.d. Template Information

1 c2rn7A_ 99.8 19 PDB header:unknown function Chain: A: PDB Molecule:is629 orfa; PDBTitle: nmr solution structure of tnpe protein from shigella2 flexneri. northeast structural genomics target sfr125 2 d2jn6a1 99.8 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Cgl2762-like 3 c2elhA_ 98.3 20 PDB header:dna binding protein Chain: A: PDB Molecule:cg11849-pa; PDBTitle: solution structure of the cenp-b n-terminal dna-binding2 domain of fruit fly distal antenna cg11849-pa 4 c1hlvA_ 98.2 15 PDB header:dna binding protein/dna Chain: A: PDB Molecule:major centromere autoantigen b; PDBTitle: crystal structure of cenp-b(1-129) complexed with the cenp-2 b box dna 5 d1pdnc_ 98.1 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 6 c6paxA_ 98.0 12 PDB header:gene regulation/dna Chain: A: PDB Molecule:homeobox protein pax-6; PDBTitle: crystal structure of the human pax-6 paired domain-dna2 complex reveals a general model for pax protein-dna3 interactions 7 d6paxa1 98.0 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 8 d1k78a1 98.0 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 9 c1u78A_ 97.9 11 PDB header:dna binding protein/dna Chain: A: PDB Molecule:transposable element tc3 transposase; PDBTitle: structure of the bipartite dna-binding domain of tc32 transposase bound to transposon dna 10 d1hlva1 97.9 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Centromere-binding 11 d1bw6a_ 97.8 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Centromere-binding 12 c3hefB_ 97.4 13 PDB header:viral protein Chain: B: PDB Molecule:gene 1 protein; PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit 13 c2gloA_ 97.3 22 PDB header:transcription/dna Chain: A: PDB Molecule:brinker cg9653-pa; PDBTitle: solution structure of the brinker dna binding domain in2 complex with the omb enhancer 14 d2coba1 97.1 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Psq domain 15 c2k27A_ 96.6 10 PDB header:transcription regulator Chain: A: PDB Molecule:paired box protein pax-8; PDBTitle: solution structure of human pax8 paired box domain 16 c2w48D_ 96.2 17 PDB header:transcription Chain: D: PDB Molecule:sorbitol operon regulator; PDBTitle: crystal structure of the full-length sorbitol operon2 regulator sorc from klebsiella pneumoniae 17 d2ao9a1 96.1 31 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Nanomeric phage protein-like 18 c2r0qF_ 95.4 11 PDB header:recombination/dna Chain: F: PDB Molecule:putative transposon tn552 dna-invertase bin3; PDBTitle: crystal structure of a serine recombinase- dna regulatory2 complex 19 d1ntca_ 95.3 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 20 d1fipa_ 95.2 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 21 c1iufA_ not modelled 95.1 8 PDB header:dna binding protein Chain: A: PDB Molecule:centromere abp1 protein; PDBTitle: low resolution solution structure of the two dna-binding2 domains in schizosaccharomyces pombe abp1 protein 22 d1umqa_ not modelled 94.8 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 23 c1umqA_ not modelled 94.8 24 PDB header:dna-binding protein Chain: A: PDB Molecule:photosynthetic apparatus regulatory protein; PDBTitle: solution structure and dna binding of the effector domain2 from the global regulator prra(rega) from r. sphaeroides:3 insights into dna binding specificity 24 d1etxa_ not modelled 94.8 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 25 c2ao9H_ not modelled 94.7 26 PDB header:structural genomics, unknown function Chain: H: PDB Molecule:phage protein; PDBTitle: structural genomics, the crystal structure of a phage protein2 (phbc6a51) from bacillus cereus atcc 14579 26 d1ocpa_ not modelled 94.7 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 27 c2l9rA_ not modelled 94.5 18 PDB header:transcription Chain: A: PDB Molecule:homeobox protein nkx-3.1; PDBTitle: solution nmr structure of homeobox domain of homeobox protein nkx-3.12 from homo sapiens, northeast structural genomics consortium target3 hr6470a 28 d1gt0c1 not modelled 94.2 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 29 c3e7lD_ not modelled 94.2 23 PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator (ntrc family); PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain 30 d2ezla_ not modelled 94.2 22 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 31 c2gm4B_ not modelled 94.0 13 PDB header:recombination, dna Chain: B: PDB Molecule:transposon gamma-delta resolvase; PDBTitle: an activated, tetrameric gamma-delta resolvase: hin chimaera bound to2 cleaved dna 32 c2da1A_ not modelled 93.7 16 PDB header:transcription Chain: A: PDB Molecule:alpha-fetoprotein enhancer binding protein; PDBTitle: solution structure of the first homeobox domain of at-2 binding transcription factor 1 (atbf1) 33 d2cuea1 not modelled 93.7 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 34 d1rzsa_ not modelled 93.7 14 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 35 c2da2A_ not modelled 93.7 11 PDB header:transcription Chain: A: PDB Molecule:alpha-fetoprotein enhancer binding protein; PDBTitle: solution structure of the second homeobox domain of at-2 binding transcription factor 1 (atbf1) 36 c2dmuA_ not modelled 93.6 23 PDB header:dna binding protein Chain: A: PDB Molecule:homeobox protein goosecoid; PDBTitle: solution structure of the homeobox domain of homeobox2 protein goosecoid 37 c2dmsA_ not modelled 93.6 18 PDB header:dna binding protein Chain: A: PDB Molecule:homeobox protein otx2; PDBTitle: solution structure of the homeobox domain of homeobox2 protein otx2 38 d2e1oa1 not modelled 93.5 27 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 39 d2craa1 not modelled 93.1 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 40 c2pbxB_ not modelled 93.1 35 PDB header:transcription Chain: B: PDB Molecule:hemagglutinin/protease regulatory protein; PDBTitle: vibrio cholerae hapr 41 c1or7A_ not modelled 93.0 5 PDB header:transcription Chain: A: PDB Molecule:rna polymerase sigma-e factor; PDBTitle: crystal structure of escherichia coli sigmae with the cytoplasmic2 domain of its anti-sigma rsea 42 d1b8ia_ not modelled 93.0 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 43 d1ahdp_ not modelled 93.0 27 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 44 d1or7a1 not modelled 92.8 5 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 45 d1bw5a_ not modelled 92.8 7 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 46 c3a01A_ not modelled 92.8 27 PDB header:gene regulation/dna Chain: A: PDB Molecule:homeodomain-containing protein; PDBTitle: crystal structure of aristaless and clawless homeodomains bound to dna 47 c3mzyA_ not modelled 92.7 20 PDB header:rna binding protein Chain: A: PDB Molecule:rna polymerase sigma-h factor; PDBTitle: the crystal structure of the rna polymerase sigma-h factor from2 fusobacterium nucleatum to 2.5a 48 d1wh7a_ not modelled 92.7 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 49 c2djnA_ not modelled 92.7 23 PDB header:transcription Chain: A: PDB Molecule:homeobox protein dlx-5; PDBTitle: the solution structure of the homeobox domain of human2 homeobox protein dlx-5 50 d1ig7a_ not modelled 92.7 22 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 51 d1zq3p1 not modelled 92.7 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 52 d1p7ia_ not modelled 92.6 25 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 53 c2k40A_ not modelled 92.6 17 PDB header:dna binding protein Chain: A: PDB Molecule:homeobox expressed in es cells 1; PDBTitle: nmr structure of hesx-1 homeodomain double mutant r31l/e42l 54 d2hddb_ not modelled 92.5 27 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 55 c2o8xA_ not modelled 92.5 10 PDB header:transcription Chain: A: PDB Molecule:probable rna polymerase sigma-c factor; PDBTitle: crystal structure of the "-35 element" promoter recognition domain of2 mycobacterium tuberculosis sigc 56 d1fjla_ not modelled 92.5 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 57 d1wh5a_ not modelled 92.4 27 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 58 c3bd1B_ not modelled 92.3 30 PDB header:transcription Chain: B: PDB Molecule:cro protein; PDBTitle: structure of the cro protein from putative prophage element xfaso 1 in2 xylella fastidiosa strain ann-1 59 d1vnda_ not modelled 92.3 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 60 d1octc1 not modelled 92.3 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 61 d1f43a_ not modelled 92.2 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 62 d1rp3a2 not modelled 92.1 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 63 d1nk3p_ not modelled 92.1 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 64 d1fjlb_ not modelled 92.1 22 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 65 d1etob_ not modelled 92.0 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 66 d1ftza_ not modelled 92.0 28 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 67 c1s7eA_ not modelled 91.9 23 PDB header:transcription Chain: A: PDB Molecule:hepatocyte nuclear factor 6; PDBTitle: solution structure of hnf-6 68 d1au7a1 not modelled 91.8 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 69 d1ztra1 not modelled 91.7 29 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 70 d1xsva_ not modelled 91.6 8 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like 71 d1ftta_ not modelled 91.6 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 72 d1yz8p1 not modelled 91.6 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 73 d1pufa_ not modelled 91.5 25 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 74 c3d1nK_ not modelled 91.5 23 PDB header:transcription regulator/dna Chain: K: PDB Molecule:pou domain, class 6, transcription factor 1; PDBTitle: structure of human brn-5 transcription factor in complex2 with corticotrophin-releasing hormone gene promoter 75 d1jgga_ not modelled 91.4 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 76 c2dmtA_ not modelled 91.4 19 PDB header:dna binding protein Chain: A: PDB Molecule:homeobox protein barh-like 1; PDBTitle: solution structure of the homeobox domain of homeobox2 protein barh-like 1 77 c2vz4A_ not modelled 91.4 13 PDB header:transcription Chain: A: PDB Molecule:hth-type transcriptional activator tipa; PDBTitle: the n-terminal domain of merr-like protein tipal bound to2 promoter dna 78 d1zs4a1 not modelled 91.3 24 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Bacteriophage CII protein 79 d1ijwc_ not modelled 91.1 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 80 c2e7xA_ not modelled 90.7 23 PDB header:transcription regulator Chain: A: PDB Molecule:150aa long hypothetical transcriptional regulator; PDBTitle: structure of the lrp/asnc like transcriptional regulator from2 sulfolobus tokodaii 7 complexed with its cognate ligand 81 c2da4A_ not modelled 90.7 20 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein dkfzp686k21156; PDBTitle: solution structure of the homeobox domain of the2 hypothetical protein, dkfzp686k21156 82 c3hugA_ not modelled 90.6 18 PDB header:transcription/membrane protein Chain: A: PDB Molecule:rna polymerase sigma factor; PDBTitle: crystal structure of mycobacterium tuberculosis anti-sigma factor rsla2 in complex with -35 promoter binding domain of sigl 83 c2kt0A_ not modelled 90.4 18 PDB header:transcription regulation Chain: A: PDB Molecule:homeobox protein nanog; PDBTitle: solution structure of human stem cell transcription factor nanog2 homeodomain fragment 84 c2p6tH_ not modelled 90.4 10 PDB header:transcription Chain: H: PDB Molecule:transcriptional regulator, lrp/asnc family; PDBTitle: crystal structure of transcriptional regulator nmb0573 and l-leucine2 complex from neisseria meningitidis 85 c2cg4B_ not modelled 90.4 8 PDB header:transcription Chain: B: PDB Molecule:regulatory protein asnc; PDBTitle: structure of e.coli asnc 86 c2da5A_ not modelled 90.3 14 PDB header:dna binding protein Chain: A: PDB Molecule:zinc fingers and homeoboxes protein 3; PDBTitle: solution structure of the second homeobox domain of zinc2 fingers and homeoboxes protein 3 (triple homeobox 13 protein) 87 d1hcra_ not modelled 90.3 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 88 d1du6a_ not modelled 90.1 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 89 c3i4pA_ not modelled 90.0 12 PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, asnc family; PDBTitle: crystal structure of asnc family transcriptional regulator from2 agrobacterium tumefaciens 90 d2ecba1 not modelled 90.0 9 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 91 c2cfxD_ not modelled 89.9 5 PDB header:transcription Chain: D: PDB Molecule:hth-type transcriptional regulator lrpc; PDBTitle: structure of b.subtilis lrpc 92 c2ia0A_ not modelled 89.9 18 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative hth-type transcriptional regulator pf0864; PDBTitle: transcriptional regulatory protein pf0864 from pyrococcus furiosus a2 member of the asnc family (pf0864) 93 d1hdpa_ not modelled 89.9 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 94 c2dmqA_ not modelled 89.8 16 PDB header:dna binding protein Chain: A: PDB Molecule:lim/homeobox protein lhx9; PDBTitle: solution structure of the homeobox domain of lim/homeobox2 protein lhx9 95 d2ecca1 not modelled 89.7 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 96 c3l1pA_ not modelled 89.6 20 PDB header:transcription/dna Chain: A: PDB Molecule:pou domain, class 5, transcription factor 1; PDBTitle: pou protein:dna complex 97 c2da3A_ not modelled 89.5 18 PDB header:transcription Chain: A: PDB Molecule:alpha-fetoprotein enhancer binding protein; PDBTitle: solution structure of the third homeobox domain of at-2 binding transcription factor 1 (atbf1) 98 c2vbzA_ not modelled 89.5 10 PDB header:dna-binding protein Chain: A: PDB Molecule:transcriptional regulatory protein; PDBTitle: feast or famine regulatory protein (rv3291c)from m.2 tuberculosis complexed with l-tryptophan 99 d1b72a_ not modelled 89.4 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 100 c2kpjA_ not modelled 89.4 9 PDB header:transcription regulator Chain: A: PDB Molecule:sos-response transcriptional repressor, lexa; PDBTitle: solution structure of protein sos-response transcriptional2 repressor, lexa from eubacterium rectale. northeast3 structural genomics consortium target err9a 101 d1q06a_ not modelled 88.9 13 Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:DNA-binding N-terminal domain of transcription activators 102 c2krfB_ not modelled 88.6 13 PDB header:transcription Chain: B: PDB Molecule:transcriptional regulatory protein coma; PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a 103 c1hf0A_ not modelled 88.5 20 PDB header:transcription factor Chain: A: PDB Molecule:octamer-binding transcription factor 1; PDBTitle: crystal structure of the dna-binding domain of oct-1 bound2 to dna as a dimer 104 d1ulya_ not modelled 88.4 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Hypothetical protein PH1932 105 d1pufb_ not modelled 88.3 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 106 d1biaa1 not modelled 88.2 5 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Biotin repressor-like 107 d2esna1 not modelled 88.1 22 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:LysR-like transcriptional regulators 108 d1e3oc1 not modelled 88.1 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 109 c3op9A_ not modelled 88.0 16 PDB header:transcription regulator Chain: A: PDB Molecule:pli0006 protein; PDBTitle: crystal structure of transcriptional regulator from listeria innocua 110 c1rp3G_ not modelled 87.7 10 PDB header:transcription Chain: G: PDB Molecule:rna polymerase sigma factor sigma-28 (flia); PDBTitle: cocrystal structure of the flagellar sigma/anti-sigma2 complex, sigma-28/flgm 111 c3e7qB_ not modelled 87.4 4 PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator; PDBTitle: the crystal structure of the putative transcriptional regulator from2 pseudomonas aeruginosa pao1 112 c2l4aA_ not modelled 87.0 13 PDB header:dna binding protein Chain: A: PDB Molecule:leucine responsive regulatory protein; PDBTitle: nmr structure of the dna-binding domain of e.coli lrp 113 d1adra_ not modelled 87.0 17 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 114 d1x2na1 not modelled 86.6 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 115 c1i1gA_ not modelled 86.6 18 PDB header:transcription Chain: A: PDB Molecule:transcriptional regulator lrpa; PDBTitle: crystal structure of the lrp-like transcriptional regulator from the2 archaeon pyrococcus furiosus 116 d2cg4a1 not modelled 86.6 8 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 117 d1s7ea1 not modelled 86.5 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 118 c2dn0A_ not modelled 86.2 20 PDB header:transcription Chain: A: PDB Molecule:zinc fingers and homeoboxes protein 3; PDBTitle: solution structure of the second homeobox domain of human2 zinc fingers and homeoboxes protein 3 119 d2oa4a1 not modelled 86.2 8 Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:SPO1678-like 120 c2jmlA_ not modelled 86.1 15 PDB header:transcription Chain: A: PDB Molecule:dna binding domain/transcriptional regulator; PDBTitle: solution structure of the n-terminal domain of cara repressor

Binding site prediction

Due to computational demand, binding site predictions are not run for batch jobs

If you want to predict binding sites, please manually submit your model of choice to 3DLigandSite

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Phyre is for academic use only

Please cite: Protein structure prediction on the web: a case study using the Phyre server
Kelley LA and Sternberg MJE. Nature Protocols 4, 363 - 371 (2009) [pdf] [Import into BibTeX]
If you use the binding site predictions from 3DLigandSite, please also cite:
3DLigandSite: predicting ligand-binding sites using similar structures.
Wass MN, Kelley LA and Sternberg MJ Nucleic Acids Research 38, W469-73 (2010) [PubMed]
© Structural Bioinformatics Group Imperial College London Lawrence Kelley, Benjamin Jefferys Disclaimer Terms and Conditions	Component software Template detection: HHpred 1.51 Secondary structure prediction: Psi-pred 2.5 Disorder prediction: Disopred 2.4 Transmembrane prediction: Memsat_SVM Multi-template modelling and ab initio: Poing 1.0