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4FVL
Asym. Unit
Info
Asym.Unit (151 KB)
Biol.Unit 1 (73 KB)
Biol.Unit 2 (74 KB)
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(1)
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
[
close entry info
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Hetero Components
(6, 64)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
1g: CALCIUM ION (CAg)
1h: CALCIUM ION (CAh)
1i: CALCIUM ION (CAi)
1j: CALCIUM ION (CAj)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
3i: GLYCEROL (GOLi)
3j: GLYCEROL (GOLj)
4a: DI(HYDROXYETHYL)ETHER (PEGa)
4b: DI(HYDROXYETHYL)ETHER (PEGb)
4c: DI(HYDROXYETHYL)ETHER (PEGc)
4d: DI(HYDROXYETHYL)ETHER (PEGd)
4e: DI(HYDROXYETHYL)ETHER (PEGe)
4f: DI(HYDROXYETHYL)ETHER (PEGf)
4g: DI(HYDROXYETHYL)ETHER (PEGg)
4h: DI(HYDROXYETHYL)ETHER (PEGh)
4i: DI(HYDROXYETHYL)ETHER (PEGi)
5a: S-1,2-PROPANEDIOL (PGOa)
5aa: S-1,2-PROPANEDIOL (PGOaa)
5ab: S-1,2-PROPANEDIOL (PGOab)
5b: S-1,2-PROPANEDIOL (PGOb)
5c: S-1,2-PROPANEDIOL (PGOc)
5d: S-1,2-PROPANEDIOL (PGOd)
5e: S-1,2-PROPANEDIOL (PGOe)
5f: S-1,2-PROPANEDIOL (PGOf)
5g: S-1,2-PROPANEDIOL (PGOg)
5h: S-1,2-PROPANEDIOL (PGOh)
5i: S-1,2-PROPANEDIOL (PGOi)
5j: S-1,2-PROPANEDIOL (PGOj)
5k: S-1,2-PROPANEDIOL (PGOk)
5l: S-1,2-PROPANEDIOL (PGOl)
5m: S-1,2-PROPANEDIOL (PGOm)
5n: S-1,2-PROPANEDIOL (PGOn)
5o: S-1,2-PROPANEDIOL (PGOo)
5p: S-1,2-PROPANEDIOL (PGOp)
5q: S-1,2-PROPANEDIOL (PGOq)
5r: S-1,2-PROPANEDIOL (PGOr)
5s: S-1,2-PROPANEDIOL (PGOs)
5t: S-1,2-PROPANEDIOL (PGOt)
5u: S-1,2-PROPANEDIOL (PGOu)
5v: S-1,2-PROPANEDIOL (PGOv)
5w: S-1,2-PROPANEDIOL (PGOw)
5x: S-1,2-PROPANEDIOL (PGOx)
5y: S-1,2-PROPANEDIOL (PGOy)
5z: S-1,2-PROPANEDIOL (PGOz)
6a: ZINC ION (ZNa)
6b: ZINC ION (ZNb)
6c: ZINC ION (ZNc)
6d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
10
Ligand/Ion
CALCIUM ION
2
CL
3
Ligand/Ion
CHLORIDE ION
3
GOL
10
Ligand/Ion
GLYCEROL
4
PEG
9
Ligand/Ion
DI(HYDROXYETHYL)ETHER
5
PGO
28
Ligand/Ion
S-1,2-PROPANEDIOL
6
ZN
4
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(62, 62)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
48: FC3 (SOFTWARE)
49: FC4 (SOFTWARE)
50: FC5 (SOFTWARE)
51: FC6 (SOFTWARE)
52: FC7 (SOFTWARE)
53: FC8 (SOFTWARE)
54: FC9 (SOFTWARE)
55: GC1 (SOFTWARE)
56: GC2 (SOFTWARE)
57: GC3 (SOFTWARE)
58: GC4 (SOFTWARE)
59: GC5 (SOFTWARE)
60: GC6 (SOFTWARE)
61: GC7 (SOFTWARE)
62: GC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:222 , HIS A:226 , HIS A:232 , SER C:45 , HOH C:204
BINDING SITE FOR RESIDUE ZN A 501
02
AC2
SOFTWARE
HIS A:172 , ASP A:174 , HIS A:187 , HIS A:200
BINDING SITE FOR RESIDUE ZN A 502
03
AC3
SOFTWARE
ASP A:179 , GLY A:180 , SER A:182 , LEU A:184 , ASP A:202 , GLU A:205
BINDING SITE FOR RESIDUE CA A 503
04
AC4
SOFTWARE
ASP A:162 , ASN A:194 , GLY A:196 , ASP A:198 , HOH A:619 , HOH A:663
BINDING SITE FOR RESIDUE CA A 504
05
AC5
SOFTWARE
ASP A:291 , ASP A:335 , SER A:383 , ASP A:432 , HOH A:605 , HOH A:612 , HOH A:669
BINDING SITE FOR RESIDUE CA A 505
06
AC6
SOFTWARE
ILE A:293 , ALA A:337 , ALA A:385 , VAL A:434 , CL A:508 , CL A:509
BINDING SITE FOR RESIDUE CA A 506
07
AC7
SOFTWARE
ASP A:128 , ASP A:203 , GLU A:205
BINDING SITE FOR RESIDUE CA A 507
08
AC8
SOFTWARE
ALA A:292 , ILE A:293 , ALA A:337 , ALA A:385 , ALA A:433 , VAL A:434 , CA A:506
BINDING SITE FOR RESIDUE CL A 508
09
AC9
SOFTWARE
ILE A:293 , THR A:294 , CA A:506 , HOH A:621 , HOH A:647
BINDING SITE FOR RESIDUE CL A 509
10
BC1
SOFTWARE
LYS 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:520
BINDING SITE FOR RESIDUE GOL A 510
11
BC2
SOFTWARE
SER A:289 , LEU A:290 , ASP A:291 , ASP A:432
BINDING SITE FOR RESIDUE GOL A 512
12
BC3
SOFTWARE
THR A:247 , MET A:253 , ARG A:306
BINDING SITE FOR RESIDUE PGO A 513
13
BC4
SOFTWARE
PRO 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:202
BINDING SITE FOR RESIDUE PGO A 514
14
BC5
SOFTWARE
ASP A:270
BINDING SITE FOR RESIDUE PGO A 515
15
BC6
SOFTWARE
GLY A:439 , PGO A:517 , ASP B:128
BINDING SITE FOR RESIDUE PGO A 516
16
BC7
SOFTWARE
TYR A:440 , TRP A:455 , PGO A:516 , HOH A:675 , PRO B:127
BINDING SITE FOR RESIDUE PGO A 517
17
BC8
SOFTWARE
GLU A:389 , THR A:391 , GLY A:392
BINDING SITE FOR RESIDUE PGO A 518
18
BC9
SOFTWARE
PRO A:281 , ASP A:282 , ASP A:285 , SER A:287 , LEU A:288 , LYS A:304 , PEG A:531
BINDING SITE FOR RESIDUE PGO A 519
19
CC1
SOFTWARE
LYS A:136 , SER A:209 , ASN A:215 , GOL A:510 , HOH A:650
BINDING SITE FOR RESIDUE PGO A 520
20
CC2
SOFTWARE
THR A:208 , SER A:210 , HOH A:680 , TRP B:455
BINDING SITE FOR RESIDUE PGO A 521
21
CC3
SOFTWARE
GLN A:401 , PRO A:417
BINDING SITE FOR RESIDUE PGO A 522
22
CC4
SOFTWARE
TYR A:125 , HIS A:131 , LEU A:419
BINDING SITE FOR RESIDUE PGO A 523
23
CC5
SOFTWARE
SER A:295 , GLU A:339 , PRO A:341 , HIS A:387 , GLU A:389 , GLU A:436 , HOH A:647
BINDING SITE FOR RESIDUE PGO A 524
24
CC6
SOFTWARE
TYR A:440 , SER A:453 , TRP A:455 , SER A:456 , VAL A:460
BINDING SITE FOR RESIDUE PGO A 525
25
CC7
SOFTWARE
TYR A:416 , ARG A:418 , ASP A:423
BINDING SITE FOR RESIDUE PGO A 526
26
CC8
SOFTWARE
TYR A:366 , PRO A:367
BINDING SITE FOR RESIDUE PGO A 527
27
CC9
SOFTWARE
THR A:300 , LEU A:311 , ILE A:468 , TRP A:470 , HOH A:651 , HOH A:654
BINDING SITE FOR RESIDUE PEG A 528
28
DC1
SOFTWARE
GLY A:248 , LYS A:324 , PRO A:331 , ASN A:332 , ARG A:333 , ARG A:350 , GLU D:33
BINDING SITE FOR RESIDUE PEG A 529
29
DC2
SOFTWARE
THR A:280 , ASP A:282
BINDING SITE FOR RESIDUE PEG A 530
30
DC3
SOFTWARE
SER A:287 , LEU A:288 , SER A:289 , LYS A:304 , GLY A:446 , PRO A:447 , PGO A:519
BINDING SITE FOR RESIDUE PEG A 531
31
DC4
SOFTWARE
PRO A:313 , GLN A:314 , SER A:325 , PRO C:49 , THR C:50
BINDING SITE FOR RESIDUE PEG A 532
32
DC5
SOFTWARE
HIS B:222 , HIS B:226 , HIS B:232 , SER D:45 , HOH D:207
BINDING SITE FOR RESIDUE ZN B 501
33
DC6
SOFTWARE
HIS B:172 , ASP B:174 , HIS B:187 , HIS B:200
BINDING SITE FOR RESIDUE ZN B 502
34
DC7
SOFTWARE
ASP B:179 , GLY B:180 , SER B:182 , LEU B:184 , ASP B:202 , GLU B:205
BINDING SITE FOR RESIDUE CA B 503
35
DC8
SOFTWARE
ASP B:162 , ASN B:194 , GLY B:196 , ASP B:198 , HOH B:633 , HOH B:713
BINDING SITE FOR RESIDUE CA B 504
36
DC9
SOFTWARE
ASP B:291 , ASP B:335 , SER B:383 , ASP B:432 , HOH B:606 , HOH B:615 , HOH B:661
BINDING SITE FOR RESIDUE CA B 505
37
EC1
SOFTWARE
ILE B:293 , ALA B:337 , ALA B:385 , VAL B:434 , CL B:508 , HOH B:617
BINDING SITE FOR RESIDUE CA B 506
38
EC2
SOFTWARE
ASP B:128 , ASP B:203 , GLU B:205
BINDING SITE FOR RESIDUE CA B 507
39
EC3
SOFTWARE
ILE B:293 , ALA B:337 , ALA B:385 , VAL B:434 , CA B:506
BINDING SITE FOR RESIDUE CL B 508
40
EC4
SOFTWARE
GLU B:133 , LYS B:136 , LYS B:140 , SER B:209 , ASN B:215 , GOL B:513
BINDING SITE FOR RESIDUE GOL B 509
41
EC5
SOFTWARE
HIS B:343 , ASN B:358 , HOH B:690
BINDING SITE FOR RESIDUE GOL B 510
42
EC6
SOFTWARE
PRO A:464 , ASN B:445 , ILE B:448
BINDING SITE FOR RESIDUE GOL B 511
43
EC7
SOFTWARE
ARG 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:625
BINDING SITE FOR RESIDUE GOL B 512
44
EC8
SOFTWARE
LYS B:140 , ASN B:215 , TYR B:246 , GLY B:248 , LYS B:249 , SER B:250 , PHE B:252 , GOL B:509
BINDING SITE FOR RESIDUE GOL B 513
45
EC9
SOFTWARE
LYS B:380 , SER B:398
BINDING SITE FOR RESIDUE GOL B 514
46
FC1
SOFTWARE
PRO B:313 , LYS B:437 , HOH B:637 , HOH B:658 , PRO D:49 , THR D:50
BINDING SITE FOR RESIDUE GOL B 515
47
FC2
SOFTWARE
LYS B:234 , ASP B:235 , PRO B:236 , HOH B:687
BINDING SITE FOR RESIDUE PGO B 516
48
FC3
SOFTWARE
TYR B:195 , ASP B:198 , HIS B:200
BINDING SITE FOR RESIDUE PGO B 517
49
FC4
SOFTWARE
PRO B:376 , GLU B:378 , GLN B:401
BINDING SITE FOR RESIDUE PGO B 518
50
FC5
SOFTWARE
SER B:146 , THR B:149 , PRO B:150 , LEU B:151 , HOH B:715
BINDING SITE FOR RESIDUE PGO B 519
51
FC6
SOFTWARE
HIS B:232 , SER B:233 , LYS B:234 , PRO B:242 , PEG D:101
BINDING SITE FOR RESIDUE PGO B 520
52
FC7
SOFTWARE
THR B:110 , LYS B:112 , SER B:114 , GLY B:192 , HOH B:708
BINDING SITE FOR RESIDUE PGO B 521
53
FC8
SOFTWARE
TYR B:435 , LYS B:437 , GLN B:449 , MET B:463
BINDING SITE FOR RESIDUE PGO B 522
54
FC9
SOFTWARE
MET B:253 , PRO B:255 , PRO B:278 , ARG B:306
BINDING SITE FOR RESIDUE PGO B 524
55
GC1
SOFTWARE
HIS B:340 , HIS B:387 , ASP B:407 , HOH B:691
BINDING SITE FOR RESIDUE PGO B 525
56
GC2
SOFTWARE
ARG B:297 , ASP B:344
BINDING SITE FOR RESIDUE PGO B 526
57
GC3
SOFTWARE
ASP B:282 , ASP B:285
BINDING SITE FOR RESIDUE PGO B 527
58
GC4
SOFTWARE
SER B:211 , THR B:245 , TYR B:246 , HOH B:712 , HIS D:48
BINDING SITE FOR RESIDUE PEG B 528
59
GC5
SOFTWARE
TYR B:104 , HOH B:669
BINDING SITE FOR RESIDUE PEG B 529
60
GC6
SOFTWARE
PRO 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:692
BINDING SITE FOR RESIDUE PEG B 530
61
GC7
SOFTWARE
ALA C:39 , ARG C:41 , TYR C:42
BINDING SITE FOR RESIDUE PGO C 101
62
GC8
SOFTWARE
PRO B:242 , PGO B:520 , ARG D:44 , SER D:45 , TYR D:47 , HOH D:206 , HOH D:210
BINDING SITE FOR RESIDUE PEG D 101
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
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CATH Domains
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all CATH domains
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Pfam Domains
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