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(-) Description

Title :  HUMAN COLLAGENASE 3 (MMP-13) FULL FORM WITH PEPTIDES FROM PRO-DOMAIN
 
Authors :  E. A. Stura, L. Vera, R. Visse, H. Nagase, V. Dive
Date :  29 Jun 12  (Deposition) - 21 Aug 13  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.44
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Protein-Peptide Complex, Collagenase, Cleavage With Mmp3, Hydrolase, Pro-Peptide, Metzincin, Zinc Metalloprotease, Collagen Cleavage, Collagen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. A. Stura, R. Visse, P. Cuniasse, V. Dive, H. Nagase
Crystal Structure Of Full-Length Human Collagenase 3 (Mmp-13) With Peptides In The Active Site Defines Exosites In The Catalytic Domain.
Faseb J. V. 27 4395 2013
PubMed-ID: 23913860  |  Reference-DOI: 10.1096/FJ.13-233601

(-) Compounds

Molecule 1 - COLLAGENASE 3
    Chains: A, B
    EC Number: 3.4.24.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: INACTIVE FULL FORM (UNP RESIDUES 104-471)
    Gene: MMP13
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MATRIX METALLOPROTEINASE-13, MMP-13
 
Molecule 2 - COLLAGENASE 3, PRO-DOMAIN PEPTIDE
    Chains: C, D
    EC Number: 3.4.24.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: PRO-DOMAIN FRAGMENT (UNP RESIDUES 31-50)
    Gene: MMP13
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MATRIX METALLOPROTEINASE-13, MMP-13

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 64)

Asymmetric Unit (6, 64)
No.NameCountTypeFull Name
1CA10Ligand/IonCALCIUM ION
2CL3Ligand/IonCHLORIDE ION
3GOL10Ligand/IonGLYCEROL
4PEG9Ligand/IonDI(HYDROXYETHYL)ETHER
5PGO28Ligand/IonS-1,2-PROPANEDIOL
6ZN4Ligand/IonZINC ION
Biological Unit 1 (3, 24)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3GOL3Ligand/IonGLYCEROL
4PEG5Ligand/IonDI(HYDROXYETHYL)ETHER
5PGO16Ligand/IonS-1,2-PROPANEDIOL
6ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 23)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3GOL7Ligand/IonGLYCEROL
4PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
5PGO12Ligand/IonS-1,2-PROPANEDIOL
6ZN-1Ligand/IonZINC ION

(-) Sites  (62, 62)

Asymmetric Unit (62, 62)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:222 , HIS A:226 , HIS A:232 , SER C:45 , HOH C:204BINDING SITE FOR RESIDUE ZN A 501
02AC2SOFTWAREHIS A:172 , ASP A:174 , HIS A:187 , HIS A:200BINDING SITE FOR RESIDUE ZN A 502
03AC3SOFTWAREASP A:179 , GLY A:180 , SER A:182 , LEU A:184 , ASP A:202 , GLU A:205BINDING SITE FOR RESIDUE CA A 503
04AC4SOFTWAREASP A:162 , ASN A:194 , GLY A:196 , ASP A:198 , HOH A:619 , HOH A:663BINDING SITE FOR RESIDUE CA A 504
05AC5SOFTWAREASP A:291 , ASP A:335 , SER A:383 , ASP A:432 , HOH A:605 , HOH A:612 , HOH A:669BINDING SITE FOR RESIDUE CA A 505
06AC6SOFTWAREILE A:293 , ALA A:337 , ALA A:385 , VAL A:434 , CL A:508 , CL A:509BINDING SITE FOR RESIDUE CA A 506
07AC7SOFTWAREASP A:128 , ASP A:203 , GLU A:205BINDING SITE FOR RESIDUE CA A 507
08AC8SOFTWAREALA A:292 , ILE A:293 , ALA A:337 , ALA A:385 , ALA A:433 , VAL A:434 , CA A:506BINDING SITE FOR RESIDUE CL A 508
09AC9SOFTWAREILE A:293 , THR A:294 , CA A:506 , HOH A:621 , HOH A:647BINDING SITE FOR RESIDUE CL A 509
10BC1SOFTWARELYS A:140 , ASN A:215 , TYR A:246 , GLY A:248 , LYS A:249 , SER A:250 , HIS A:251 , PHE A:252 , PGO A:520BINDING SITE FOR RESIDUE GOL A 510
11BC2SOFTWARESER A:289 , LEU A:290 , ASP A:291 , ASP A:432BINDING SITE FOR RESIDUE GOL A 512
12BC3SOFTWARETHR A:247 , MET A:253 , ARG A:306BINDING SITE FOR RESIDUE PGO A 513
13BC4SOFTWAREPRO A:236 , GLY A:237 , ALA A:238 , ILE A:243 , THR A:245 , LEU A:322 , HOH A:631 , TYR C:46 , HOH C:202BINDING SITE FOR RESIDUE PGO A 514
14BC5SOFTWAREASP A:270BINDING SITE FOR RESIDUE PGO A 515
15BC6SOFTWAREGLY A:439 , PGO A:517 , ASP B:128BINDING SITE FOR RESIDUE PGO A 516
16BC7SOFTWARETYR A:440 , TRP A:455 , PGO A:516 , HOH A:675 , PRO B:127BINDING SITE FOR RESIDUE PGO A 517
17BC8SOFTWAREGLU A:389 , THR A:391 , GLY A:392BINDING SITE FOR RESIDUE PGO A 518
18BC9SOFTWAREPRO A:281 , ASP A:282 , ASP A:285 , SER A:287 , LEU A:288 , LYS A:304 , PEG A:531BINDING SITE FOR RESIDUE PGO A 519
19CC1SOFTWARELYS A:136 , SER A:209 , ASN A:215 , GOL A:510 , HOH A:650BINDING SITE FOR RESIDUE PGO A 520
20CC2SOFTWARETHR A:208 , SER A:210 , HOH A:680 , TRP B:455BINDING SITE FOR RESIDUE PGO A 521
21CC3SOFTWAREGLN A:401 , PRO A:417BINDING SITE FOR RESIDUE PGO A 522
22CC4SOFTWARETYR A:125 , HIS A:131 , LEU A:419BINDING SITE FOR RESIDUE PGO A 523
23CC5SOFTWARESER A:295 , GLU A:339 , PRO A:341 , HIS A:387 , GLU A:389 , GLU A:436 , HOH A:647BINDING SITE FOR RESIDUE PGO A 524
24CC6SOFTWARETYR A:440 , SER A:453 , TRP A:455 , SER A:456 , VAL A:460BINDING SITE FOR RESIDUE PGO A 525
25CC7SOFTWARETYR A:416 , ARG A:418 , ASP A:423BINDING SITE FOR RESIDUE PGO A 526
26CC8SOFTWARETYR A:366 , PRO A:367BINDING SITE FOR RESIDUE PGO A 527
27CC9SOFTWARETHR A:300 , LEU A:311 , ILE A:468 , TRP A:470 , HOH A:651 , HOH A:654BINDING SITE FOR RESIDUE PEG A 528
28DC1SOFTWAREGLY A:248 , LYS A:324 , PRO A:331 , ASN A:332 , ARG A:333 , ARG A:350 , GLU D:33BINDING SITE FOR RESIDUE PEG A 529
29DC2SOFTWARETHR A:280 , ASP A:282BINDING SITE FOR RESIDUE PEG A 530
30DC3SOFTWARESER A:287 , LEU A:288 , SER A:289 , LYS A:304 , GLY A:446 , PRO A:447 , PGO A:519BINDING SITE FOR RESIDUE PEG A 531
31DC4SOFTWAREPRO A:313 , GLN A:314 , SER A:325 , PRO C:49 , THR C:50BINDING SITE FOR RESIDUE PEG A 532
32DC5SOFTWAREHIS B:222 , HIS B:226 , HIS B:232 , SER D:45 , HOH D:207BINDING SITE FOR RESIDUE ZN B 501
33DC6SOFTWAREHIS B:172 , ASP B:174 , HIS B:187 , HIS B:200BINDING SITE FOR RESIDUE ZN B 502
34DC7SOFTWAREASP B:179 , GLY B:180 , SER B:182 , LEU B:184 , ASP B:202 , GLU B:205BINDING SITE FOR RESIDUE CA B 503
35DC8SOFTWAREASP B:162 , ASN B:194 , GLY B:196 , ASP B:198 , HOH B:633 , HOH B:713BINDING SITE FOR RESIDUE CA B 504
36DC9SOFTWAREASP B:291 , ASP B:335 , SER B:383 , ASP B:432 , HOH B:606 , HOH B:615 , HOH B:661BINDING SITE FOR RESIDUE CA B 505
37EC1SOFTWAREILE B:293 , ALA B:337 , ALA B:385 , VAL B:434 , CL B:508 , HOH B:617BINDING SITE FOR RESIDUE CA B 506
38EC2SOFTWAREASP B:128 , ASP B:203 , GLU B:205BINDING SITE FOR RESIDUE CA B 507
39EC3SOFTWAREILE B:293 , ALA B:337 , ALA B:385 , VAL B:434 , CA B:506BINDING SITE FOR RESIDUE CL B 508
40EC4SOFTWAREGLU B:133 , LYS B:136 , LYS B:140 , SER B:209 , ASN B:215 , GOL B:513BINDING SITE FOR RESIDUE GOL B 509
41EC5SOFTWAREHIS B:343 , ASN B:358 , HOH B:690BINDING SITE FOR RESIDUE GOL B 510
42EC6SOFTWAREPRO A:464 , ASN B:445 , ILE B:448BINDING SITE FOR RESIDUE GOL B 511
43EC7SOFTWAREARG A:458 , ILE A:459 , VAL A:460 , ARG A:461 , GLU B:421 , GLY B:426 , ILE B:427 , GLY B:428 , HOH B:625BINDING SITE FOR RESIDUE GOL B 512
44EC8SOFTWARELYS B:140 , ASN B:215 , TYR B:246 , GLY B:248 , LYS B:249 , SER B:250 , PHE B:252 , GOL B:509BINDING SITE FOR RESIDUE GOL B 513
45EC9SOFTWARELYS B:380 , SER B:398BINDING SITE FOR RESIDUE GOL B 514
46FC1SOFTWAREPRO B:313 , LYS B:437 , HOH B:637 , HOH B:658 , PRO D:49 , THR D:50BINDING SITE FOR RESIDUE GOL B 515
47FC2SOFTWARELYS B:234 , ASP B:235 , PRO B:236 , HOH B:687BINDING SITE FOR RESIDUE PGO B 516
48FC3SOFTWARETYR B:195 , ASP B:198 , HIS B:200BINDING SITE FOR RESIDUE PGO B 517
49FC4SOFTWAREPRO B:376 , GLU B:378 , GLN B:401BINDING SITE FOR RESIDUE PGO B 518
50FC5SOFTWARESER B:146 , THR B:149 , PRO B:150 , LEU B:151 , HOH B:715BINDING SITE FOR RESIDUE PGO B 519
51FC6SOFTWAREHIS B:232 , SER B:233 , LYS B:234 , PRO B:242 , PEG D:101BINDING SITE FOR RESIDUE PGO B 520
52FC7SOFTWARETHR B:110 , LYS B:112 , SER B:114 , GLY B:192 , HOH B:708BINDING SITE FOR RESIDUE PGO B 521
53FC8SOFTWARETYR B:435 , LYS B:437 , GLN B:449 , MET B:463BINDING SITE FOR RESIDUE PGO B 522
54FC9SOFTWAREMET B:253 , PRO B:255 , PRO B:278 , ARG B:306BINDING SITE FOR RESIDUE PGO B 524
55GC1SOFTWAREHIS B:340 , HIS B:387 , ASP B:407 , HOH B:691BINDING SITE FOR RESIDUE PGO B 525
56GC2SOFTWAREARG B:297 , ASP B:344BINDING SITE FOR RESIDUE PGO B 526
57GC3SOFTWAREASP B:282 , ASP B:285BINDING SITE FOR RESIDUE PGO B 527
58GC4SOFTWARESER B:211 , THR B:245 , TYR B:246 , HOH B:712 , HIS D:48BINDING SITE FOR RESIDUE PEG B 528
59GC5SOFTWARETYR B:104 , HOH B:669BINDING SITE FOR RESIDUE PEG B 529
60GC6SOFTWAREPRO B:236 , PHE B:241 , ILE B:243 , THR B:245 , GLN B:314 , LEU B:322 , SER B:325 , HOH B:624 , HOH B:692BINDING SITE FOR RESIDUE PEG B 530
61GC7SOFTWAREALA C:39 , ARG C:41 , TYR C:42BINDING SITE FOR RESIDUE PGO C 101
62GC8SOFTWAREPRO B:242 , PGO B:520 , ARG D:44 , SER D:45 , TYR D:47 , HOH D:206 , HOH D:210BINDING SITE FOR RESIDUE PEG D 101

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1B:284 -B:471

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:366 -Pro A:367
2Tyr A:416 -Pro A:417
3Tyr B:366 -Pro B:367
4Tyr B:416 -Pro B:417

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4FVL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FVL)

(-) Exons   (0, 0)

(no "Exon" information available for 4FVL)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:368
                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhhh.....eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee..............eeeeee..........eeee....ee.....eehhhhhhhhhhhhhhee.......................hhhhhhhhhhhhh........................eeeee..eeeeee..eeeee.......eeeehhhhh........eeeeehhhheeeeee..eeeeee..ee.....ee.hhhh.........eeee.....eeeeee..eeeeee....ee.....eehhhhh........eeeee..eeeeee..eeeeee....eeeeeee.hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fvl A 104 YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHAFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGPGDEDPNPKHPKTPDKCDPSLSLDAITSLRGETMIFKDRFFWRLHPQQVDAELFLTKSFWPELPNRIDAAYEHPSHDLIFIFRGRKFWALNGYDILEGYPKKISELGLPKEVKKISAAVHFEDTGKTLLFSGNQVWRYDDTNHIMDKDYPRLIEEDFPGIGDKVDAVYEKNGYIYFFNGPIQFEYSIWSNRIVRVMPANSILWC 471
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463        


Chain B from PDB  Type:PROTEIN  Length:368
                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..........eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee..............eeeeee..........eeee....ee.....eehhhhhhhhhhhhhhee.......................hhhhhhhhhhhhh........................eeeee..eeeeee..eeeee.......eeee.hhh.........eeeee....eeeeee..eeeeee..ee.....ee.hhhh.........eeee.....eeeeee..eeeeee....ee.....eehhhhh........eeeee..eeeeee..eeeeee....eeeeeee.hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fvl B 104 YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHAFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGPGDEDPNPKHPKTPDKCDPSLSLDAITSLRGETMIFKDRFFWRLHPQQVDAELFLTKSFWPELPNRIDAAYEHPSHDLIFIFRGRKFWALNGYDILEGYPKKISELGLPKEVKKISAAVHFEDTGKTLLFSGNQVWRYDDTNHIMDKDYPRLIEEDFPGIGDKVDAVYEKNGYIYFFNGPIQFEYSIWSNRIVRVMPANSILWC 471
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463        


Chain C from PDB  Type:PROTEIN  Length:14
                                              
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author .......eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                 4fvl C  37 QFAERYLRSYYHPT  50
                                    46    


Chain D from PDB  Type:PROTEIN  Length:20
                                                    
               SCOP domains -------------------- SCOP domains
               CATH domains -------------------- CATH domains
               Pfam domains -------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhheeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------- SAPs(SNPs)
                    PROSITE -------------------- PROSITE
                 Transcript -------------------- Transcript
                 4fvl D  31 LSEEDLQFAERYLRSYYHPT  50
                                    40        50
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4FVL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4FVL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4FVL)

(-) Gene Ontology  (42, 42)

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  Cis Peptide Bonds
    Tyr A:366 - Pro A:367   [ RasMol ]  
    Tyr A:416 - Pro A:417   [ RasMol ]  
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 Related Entries

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        MMP13_HUMAN | P45452: 1eub 1fls 1fm1 1pex 1uc1 1xuc 1xud 1xur 1you 1ztq 2d1n 2e2d 2ow9 2ozr 2pjt 2yig 3elm 3i7g 3i7i 3kec 3kej 3kek 3kry 3ljz 3o2x 3tvc 3wv1 3wv2 3wv3 3zxh 456c 4a7b 4fu4 4g0d 4jp4 4jpa 4l19 5b5o 5b5p 5bot 5boy 5bpa 5uwk 5uwl 5uwm 5uwn 830c

(-) Related Entries Specified in the PDB File

1pex COLLAGENASE-3 (MMP-13) C-TERMINAL HEMOPEXIN-LIKE DOMAIN METALLOPROTEASE
3tvc HUMAN MMP13 IN COMPLEX WITH L-GLUTAMATE MOTIF INHIBITOR
4fu4 HUMAN COLLAGENASE 3 (MMP-13) WITH PEPTIDE FROM PRO-DOMAIN