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(-) Description

Title :  HUMAN COLLAGENASE 3 (MMP-13) WITH PEPTIDE FROM PRO-DOMAIN
 
Authors :  E. A. Stura, L. Vera, R. Visse, H. Nagase, V. Dive
Date :  28 Jun 12  (Deposition) - 21 Aug 13  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Protein-Peptide Complex, Collagenase, Collagen, Cleavage With Mmp3, Hydrolase, Pro-Peptide, Metzincin, Zinc Metalloprotease, Collagen Cleavage (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
    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 25-50)
    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  (4, 42)

Asymmetric Unit (4, 42)
No.NameCountTypeFull Name
1CA8Ligand/IonCALCIUM ION
2CL4Ligand/IonCHLORIDE ION
3EDO26Ligand/Ion1,2-ETHANEDIOL
4ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3EDO12Ligand/Ion1,2-ETHANEDIOL
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 14)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3EDO14Ligand/Ion1,2-ETHANEDIOL
4ZN-1Ligand/IonZINC ION

(-) Sites  (42, 42)

Asymmetric Unit (42, 42)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:222 , HIS A:226 , HIS A:232 , ALA C:39 , GLU C:40 , CL C:101BINDING 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:198BINDING SITE FOR RESIDUE CA A 504
05AC5SOFTWAREASP A:291 , ASP A:335 , SER A:383 , ASP A:432 , HOH A:610BINDING SITE FOR RESIDUE CA A 505
06AC6SOFTWAREILE A:293 , ALA A:337 , ALA A:385 , VAL A:434 , CL A:507BINDING SITE FOR RESIDUE CA A 506
07AC7SOFTWAREILE A:293 , ALA A:337 , ALA A:385 , VAL A:434 , CA A:506BINDING SITE FOR RESIDUE CL A 507
08AC8SOFTWARESER A:467BINDING SITE FOR RESIDUE EDO A 508
09AC9SOFTWARETYR A:440 , GLU A:451 , ARG A:461 , ARG C:44BINDING SITE FOR RESIDUE EDO A 509
10BC1SOFTWARETYR A:416 , ASP A:423 , EDO A:514BINDING SITE FOR RESIDUE EDO A 510
11BC2SOFTWAREHOH A:609BINDING SITE FOR RESIDUE EDO A 511
12BC3SOFTWAREASN A:194 , TYR A:195BINDING SITE FOR RESIDUE EDO A 512
13BC4SOFTWARETHR A:247 , MET A:253 , ARG A:306BINDING SITE FOR RESIDUE EDO A 513
14BC5SOFTWAREEDO A:510BINDING SITE FOR RESIDUE EDO A 514
15BC6SOFTWARETYR A:440 , TRP A:455BINDING SITE FOR RESIDUE EDO A 515
16BC7SOFTWARETYR A:104 , ASN A:105 , HOH A:626BINDING SITE FOR RESIDUE EDO A 516
17BC8SOFTWAREGLN A:263 , SER A:264BINDING SITE FOR RESIDUE EDO A 517
18BC9SOFTWARELYS A:234 , ASP A:317BINDING SITE FOR RESIDUE EDO A 518
19CC1SOFTWAREHIS B:222 , HIS B:226 , HIS B:232 , SER D:45 , CL D:101BINDING SITE FOR RESIDUE ZN B 501
20CC2SOFTWAREHIS B:172 , ASP B:174 , HIS B:187 , HIS B:200BINDING SITE FOR RESIDUE ZN B 502
21CC3SOFTWAREASP B:179 , GLY B:180 , SER B:182 , LEU B:184 , ASP B:202 , GLU B:205BINDING SITE FOR RESIDUE CA B 503
22CC4SOFTWAREASP B:162 , ASN B:194 , GLY B:196 , ASP B:198BINDING SITE FOR RESIDUE CA B 504
23CC5SOFTWAREASP B:291 , ASP B:335 , SER B:383 , ASP B:432 , HOH B:636 , HOH B:653BINDING SITE FOR RESIDUE CA B 505
24CC6SOFTWAREILE B:293 , ALA B:337 , ALA B:385 , VAL B:434 , CL B:507 , HOH B:635BINDING SITE FOR RESIDUE CA B 506
25CC7SOFTWAREALA B:292 , ILE B:293 , ALA B:337 , ALA B:433 , VAL B:434 , CA B:506BINDING SITE FOR RESIDUE CL B 507
26CC8SOFTWAREPHE B:326 , GLY B:359BINDING SITE FOR RESIDUE EDO B 508
27CC9SOFTWAREASP B:128 , ASP B:203 , ASP B:204 , GLU B:205 , THR B:206BINDING SITE FOR RESIDUE EDO B 509
28DC1SOFTWARETHR B:247 , PHE B:252 , MET B:253 , PRO B:255BINDING SITE FOR RESIDUE EDO B 510
29DC2SOFTWAREPRO A:464 , ASN B:445 , ILE B:448BINDING SITE FOR RESIDUE EDO B 511
30DC3SOFTWAREPRO B:236 , THR B:280 , PRO B:281 , HOH B:645BINDING SITE FOR RESIDUE EDO B 512
31DC4SOFTWARETHR B:391 , LYS B:393 , ILE B:454BINDING SITE FOR RESIDUE EDO B 513
32DC5SOFTWARETYR B:104BINDING SITE FOR RESIDUE EDO B 514
33DC6SOFTWAREGLN B:260 , SER B:264BINDING SITE FOR RESIDUE EDO B 515
34DC7SOFTWAREGLN B:263 , GLY B:267BINDING SITE FOR RESIDUE EDO B 516
35DC8SOFTWAREGLY B:248 , LYS B:249 , SER B:250 , HIS B:251 , PHE B:252BINDING SITE FOR RESIDUE EDO B 517
36DC9SOFTWARELYS B:437 , TYR B:442 , GLN B:449 , EDO B:519BINDING SITE FOR RESIDUE EDO B 518
37EC1SOFTWARETRP B:470 , EDO B:518 , TYR D:47BINDING SITE FOR RESIDUE EDO B 519
38EC2SOFTWARESER B:146 , THR B:149 , PRO B:150 , LEU B:151 , ASN B:152 , GLY B:269 , ASP B:270 , HOH B:641BINDING SITE FOR RESIDUE EDO B 520
39EC3SOFTWAREALA A:186 , HIS A:187 , HIS A:226 , ZN A:501 , PHE C:38 , ALA C:39 , GLU C:40BINDING SITE FOR RESIDUE CL C 101
40EC4SOFTWAREARG A:297 , PRO C:49BINDING SITE FOR RESIDUE EDO C 102
41EC5SOFTWAREHIS B:222 , HIS B:226 , ZN B:501 , ARG D:44 , SER D:45 , TYR D:46BINDING SITE FOR RESIDUE CL D 101
42EC6SOFTWAREHIS B:232 , ARG D:44 , SER D:45 , TYR D:47BINDING SITE FOR RESIDUE EDO D 102

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:284 -A:471
2B:284 -B:471

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Gly A:267 -Pro A:268
2Tyr A:366 -Pro A:367
3Tyr A:416 -Pro A:417
4Tyr B:366 -Pro B:367
5Tyr B:416 -Pro B:417
6Gly C:25 -Gly C:26

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4FU4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FU4)

(-) Exons   (0, 0)

(no "Exon" information available for 4FU4)

(-) 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.....eehhhhhhhhhhhhh.ee.......................hhhhhhhhhh...........................eeeee..eeeeee..eeeee.......eeee.hhh.........eeeee....eeeeee..eeeeee..ee.....ee.hhhh.........eeeee....eeeeee..eeeeee....ee.....eehhhhh........eeeee..eeeeee..eeeeee....eeeeeee.hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fu4 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....eeeee......eeeeee..............eeeeee..........eeee....ee.....eehhhhhhhhhhhhh.ee.......................hhhhhhhhhhhhh........................eeeee..eeeeee..eeeee.......eeeehhhhh........eeeeehhhheeeeee..eeeeee..ee.....ee.hhhh.........eeee.....eeeeee..eeeeee....ee.....eehhhhh........eeeee..eeeeee..eeeeee.....eeeeee.hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fu4 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:26
                                                          
               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
                 4fu4 C  25 GGDEDDLSEEDLQFAERYLRSYYHPT  50
                                    34        44      


Chain D from PDB  Type:PROTEIN  Length:26
                                                          
               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
                 4fu4 D  25 GGDEDDLSEEDLQFAERYLRSYYHPT  50
                                    34        44
   Legend:   → Mismatch (orange background)
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  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 4FU4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4FU4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4FU4)

(-) Gene Ontology  (42, 42)

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  4fu4
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  MMP13_HUMAN | P45452
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  3.4.24.-
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        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 4fvl 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