4FVL
Human collagenase 3 (MMP-13) full form with peptides from pro-domain
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004222 | molecular_function | metalloendopeptidase activity |
| A | 0006508 | biological_process | proteolysis |
| A | 0008237 | molecular_function | metallopeptidase activity |
| A | 0008270 | molecular_function | zinc ion binding |
| A | 0031012 | cellular_component | extracellular matrix |
| B | 0004222 | molecular_function | metalloendopeptidase activity |
| B | 0006508 | biological_process | proteolysis |
| B | 0008237 | molecular_function | metallopeptidase activity |
| B | 0008270 | molecular_function | zinc ion binding |
| B | 0031012 | cellular_component | extracellular matrix |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE ZN A 501 |
| Chain | Residue |
| A | HIS222 |
| A | HIS226 |
| A | HIS232 |
| C | SER45 |
| C | HOH204 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN A 502 |
| Chain | Residue |
| A | HIS172 |
| A | ASP174 |
| A | HIS187 |
| A | HIS200 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA A 503 |
| Chain | Residue |
| A | ASP179 |
| A | GLY180 |
| A | SER182 |
| A | LEU184 |
| A | ASP202 |
| A | GLU205 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA A 504 |
| Chain | Residue |
| A | ASP162 |
| A | ASN194 |
| A | GLY196 |
| A | ASP198 |
| A | HOH619 |
| A | HOH663 |
| site_id | AC5 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE CA A 505 |
| Chain | Residue |
| A | ASP291 |
| A | ASP335 |
| A | SER383 |
| A | ASP432 |
| A | HOH605 |
| A | HOH612 |
| A | HOH669 |
| site_id | AC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA A 506 |
| Chain | Residue |
| A | ILE293 |
| A | ALA337 |
| A | ALA385 |
| A | VAL434 |
| A | CL508 |
| A | CL509 |
| site_id | AC7 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE CA A 507 |
| Chain | Residue |
| A | ASP128 |
| A | ASP203 |
| A | GLU205 |
| site_id | AC8 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE CL A 508 |
| Chain | Residue |
| A | ALA292 |
| A | ILE293 |
| A | ALA337 |
| A | ALA385 |
| A | ALA433 |
| A | VAL434 |
| A | CA506 |
| site_id | AC9 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE CL A 509 |
| Chain | Residue |
| A | ILE293 |
| A | THR294 |
| A | CA506 |
| A | HOH621 |
| A | HOH647 |
| site_id | BC1 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE GOL A 510 |
| Chain | Residue |
| A | LYS140 |
| A | ASN215 |
| A | TYR246 |
| A | GLY248 |
| A | LYS249 |
| A | SER250 |
| A | HIS251 |
| A | PHE252 |
| A | PGO520 |
| site_id | BC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE GOL A 512 |
| Chain | Residue |
| A | SER289 |
| A | LEU290 |
| A | ASP291 |
| A | ASP432 |
| site_id | BC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE PGO A 513 |
| Chain | Residue |
| A | THR247 |
| A | MET253 |
| A | ARG306 |
| site_id | BC4 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE PGO A 514 |
| Chain | Residue |
| A | PRO236 |
| A | GLY237 |
| A | ALA238 |
| A | ILE243 |
| A | THR245 |
| A | LEU322 |
| A | HOH631 |
| C | TYR46 |
| C | HOH202 |
| site_id | BC5 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE PGO A 515 |
| Chain | Residue |
| A | ASP270 |
| site_id | BC6 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE PGO A 516 |
| Chain | Residue |
| A | GLY439 |
| A | PGO517 |
| B | ASP128 |
| site_id | BC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PGO A 517 |
| Chain | Residue |
| A | TYR440 |
| A | TRP455 |
| A | PGO516 |
| A | HOH675 |
| B | PRO127 |
| site_id | BC8 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE PGO A 518 |
| Chain | Residue |
| A | GLU389 |
| A | THR391 |
| A | GLY392 |
| site_id | BC9 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE PGO A 519 |
| Chain | Residue |
| A | PRO281 |
| A | ASP282 |
| A | ASP285 |
| A | SER287 |
| A | LEU288 |
| A | LYS304 |
| A | PEG531 |
| site_id | CC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PGO A 520 |
| Chain | Residue |
| A | LYS136 |
| A | SER209 |
| A | ASN215 |
| A | GOL510 |
| A | HOH650 |
| site_id | CC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE PGO A 521 |
| Chain | Residue |
| A | SER210 |
| A | HOH680 |
| B | TRP455 |
| A | THR208 |
| site_id | CC3 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PGO A 522 |
| Chain | Residue |
| A | GLN401 |
| A | PRO417 |
| site_id | CC4 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE PGO A 523 |
| Chain | Residue |
| A | TYR125 |
| A | HIS131 |
| A | LEU419 |
| site_id | CC5 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE PGO A 524 |
| Chain | Residue |
| A | SER295 |
| A | GLU339 |
| A | PRO341 |
| A | HIS387 |
| A | GLU389 |
| A | GLU436 |
| A | HOH647 |
| site_id | CC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PGO A 525 |
| Chain | Residue |
| A | TYR440 |
| A | SER453 |
| A | TRP455 |
| A | SER456 |
| A | VAL460 |
| site_id | CC7 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE PGO A 526 |
| Chain | Residue |
| A | TYR416 |
| A | ARG418 |
| A | ASP423 |
| site_id | CC8 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PGO A 527 |
| Chain | Residue |
| A | TYR366 |
| A | PRO367 |
| site_id | CC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE PEG A 528 |
| Chain | Residue |
| A | THR300 |
| A | LEU311 |
| A | ILE468 |
| A | TRP470 |
| A | HOH651 |
| A | HOH654 |
| site_id | DC1 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE PEG A 529 |
| Chain | Residue |
| A | GLY248 |
| A | LYS324 |
| A | PRO331 |
| A | ASN332 |
| A | ARG333 |
| A | ARG350 |
| D | GLU33 |
| site_id | DC2 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PEG A 530 |
| Chain | Residue |
| A | THR280 |
| A | ASP282 |
| site_id | DC3 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE PEG A 531 |
| Chain | Residue |
| A | SER287 |
| A | LEU288 |
| A | SER289 |
| A | LYS304 |
| A | GLY446 |
| A | PRO447 |
| A | PGO519 |
| site_id | DC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PEG A 532 |
| Chain | Residue |
| A | PRO313 |
| A | GLN314 |
| A | SER325 |
| C | PRO49 |
| C | THR50 |
| site_id | DC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE ZN B 501 |
| Chain | Residue |
| B | HIS222 |
| B | HIS226 |
| B | HIS232 |
| D | SER45 |
| D | HOH207 |
| site_id | DC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN B 502 |
| Chain | Residue |
| B | HIS172 |
| B | ASP174 |
| B | HIS187 |
| B | HIS200 |
| site_id | DC7 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA B 503 |
| Chain | Residue |
| B | ASP179 |
| B | GLY180 |
| B | SER182 |
| B | LEU184 |
| B | ASP202 |
| B | GLU205 |
| site_id | DC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA B 504 |
| Chain | Residue |
| B | ASP162 |
| B | ASN194 |
| B | GLY196 |
| B | ASP198 |
| B | HOH633 |
| B | HOH713 |
| site_id | DC9 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE CA B 505 |
| Chain | Residue |
| B | ASP291 |
| B | ASP335 |
| B | SER383 |
| B | ASP432 |
| B | HOH606 |
| B | HOH615 |
| B | HOH661 |
| site_id | EC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA B 506 |
| Chain | Residue |
| B | ILE293 |
| B | ALA337 |
| B | ALA385 |
| B | VAL434 |
| B | CL508 |
| B | HOH617 |
| site_id | EC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE CA B 507 |
| Chain | Residue |
| B | ASP128 |
| B | ASP203 |
| B | GLU205 |
| site_id | EC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE CL B 508 |
| Chain | Residue |
| B | ILE293 |
| B | ALA337 |
| B | ALA385 |
| B | VAL434 |
| B | CA506 |
| site_id | EC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL B 509 |
| Chain | Residue |
| B | GLU133 |
| B | LYS136 |
| B | LYS140 |
| B | SER209 |
| B | ASN215 |
| B | GOL513 |
| site_id | EC5 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE GOL B 510 |
| Chain | Residue |
| B | HIS343 |
| B | ASN358 |
| B | HOH690 |
| site_id | EC6 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE GOL B 511 |
| Chain | Residue |
| A | PRO464 |
| B | ASN445 |
| B | ILE448 |
| site_id | EC7 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE GOL B 512 |
| Chain | Residue |
| A | ARG458 |
| A | ILE459 |
| A | VAL460 |
| A | ARG461 |
| B | GLU421 |
| B | GLY426 |
| B | ILE427 |
| B | GLY428 |
| B | HOH625 |
| site_id | EC8 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL B 513 |
| Chain | Residue |
| B | LYS140 |
| B | ASN215 |
| B | TYR246 |
| B | GLY248 |
| B | LYS249 |
| B | SER250 |
| B | PHE252 |
| B | GOL509 |
| site_id | EC9 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE GOL B 514 |
| Chain | Residue |
| B | LYS380 |
| B | SER398 |
| site_id | FC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL B 515 |
| Chain | Residue |
| B | PRO313 |
| B | LYS437 |
| B | HOH637 |
| B | HOH658 |
| D | PRO49 |
| D | THR50 |
| site_id | FC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE PGO B 516 |
| Chain | Residue |
| B | LYS234 |
| B | ASP235 |
| B | PRO236 |
| B | HOH687 |
| site_id | FC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE PGO B 517 |
| Chain | Residue |
| B | TYR195 |
| B | ASP198 |
| B | HIS200 |
| site_id | FC4 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE PGO B 518 |
| Chain | Residue |
| B | PRO376 |
| B | GLU378 |
| B | GLN401 |
| site_id | FC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PGO B 519 |
| Chain | Residue |
| B | SER146 |
| B | THR149 |
| B | PRO150 |
| B | LEU151 |
| B | HOH715 |
| site_id | FC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PGO B 520 |
| Chain | Residue |
| B | HIS232 |
| B | SER233 |
| B | LYS234 |
| B | PRO242 |
| D | PEG101 |
| site_id | FC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PGO B 521 |
| Chain | Residue |
| B | THR110 |
| B | LYS112 |
| B | SER114 |
| B | GLY192 |
| B | HOH708 |
| site_id | FC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE PGO B 522 |
| Chain | Residue |
| B | TYR435 |
| B | LYS437 |
| B | GLN449 |
| B | MET463 |
| site_id | FC9 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE PGO B 524 |
| Chain | Residue |
| B | MET253 |
| B | PRO255 |
| B | PRO278 |
| B | ARG306 |
| site_id | GC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE PGO B 525 |
| Chain | Residue |
| B | HIS340 |
| B | HIS387 |
| B | ASP407 |
| B | HOH691 |
| site_id | GC2 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PGO B 526 |
| Chain | Residue |
| B | ARG297 |
| B | ASP344 |
| site_id | GC3 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PGO B 527 |
| Chain | Residue |
| B | ASP282 |
| B | ASP285 |
| site_id | GC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PEG B 528 |
| Chain | Residue |
| B | SER211 |
| B | THR245 |
| B | TYR246 |
| B | HOH712 |
| D | HIS48 |
| site_id | GC5 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PEG B 529 |
| Chain | Residue |
| B | TYR104 |
| B | HOH669 |
| site_id | GC6 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE PEG B 530 |
| Chain | Residue |
| B | PRO236 |
| B | PHE241 |
| B | ILE243 |
| B | THR245 |
| B | GLN314 |
| B | LEU322 |
| B | SER325 |
| B | HOH624 |
| B | HOH692 |
| site_id | GC7 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE PGO C 101 |
| Chain | Residue |
| C | ALA39 |
| C | ARG41 |
| C | TYR42 |
| site_id | GC8 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE PEG D 101 |
| Chain | Residue |
| B | PRO242 |
| B | PGO520 |
| D | ARG44 |
| D | SER45 |
| D | TYR47 |
| D | HOH206 |
| D | HOH210 |
Functional Information from PROSITE/UniProt
| site_id | PS00024 |
| Number of Residues | 16 |
| Details | HEMOPEXIN Hemopexin domain signature. TKsfWpelPnRIDAAY |
| Chain | Residue | Details |
| A | THR323-TYR338 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 98 |
| Details | Repeat: {"description":"Hemopexin 1"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 92 |
| Details | Repeat: {"description":"Hemopexin 2"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 96 |
| Details | Repeat: {"description":"Hemopexin 3"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 86 |
| Details | Repeat: {"description":"Hemopexin 4"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 140 |
| Details | Region: {"description":"Interaction with TIMP2"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 42 |
| Details | Region: {"description":"Disordered","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 406 |
| Details | Region: {"description":"Interaction with collagen"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 22 |
| Details | Compositional bias: {"description":"Basic and acidic residues","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | Active site: {"evidences":[{"source":"PubMed","id":"23913860","evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI10 |
| Number of Residues | 40 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"10926524","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"10986126","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15734645","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15780611","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17196980","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17623656","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19422229","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20005097","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20726512","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22689580","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23810497","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23913860","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8969305","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI11 |
| Number of Residues | 16 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"10926524","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"10986126","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15734645","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15780611","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17196980","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17623656","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19422229","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20005097","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20726512","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22689580","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23810497","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23913860","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI12 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphotyrosine; by PKDCC","evidences":[{"source":"PubMed","id":"25171405","evidenceCode":"ECO:0000303"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI13 |
| Number of Residues | 2 |
| Details | Glycosylation: {"description":"N-linked (GlcNAc...) asparagine","evidences":[{"source":"PubMed","id":"8576151","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI14 |
| Number of Residues | 2 |
| Details | Glycosylation: {"description":"N-linked (GlcNAc...) asparagine","evidences":[{"evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
