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2PJT
Asym. Unit
Info
Asym.Unit (119 KB)
Biol.Unit 1 (31 KB)
Biol.Unit 2 (31 KB)
Biol.Unit 3 (30 KB)
Biol.Unit 4 (31 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF MMP-13 COMPLEXED WITH WAY-344
Authors
:
Z. Xu, A. Huang, F. Lovering, J. I. Levin, L. Mosyak
Date
:
16 Apr 07 (Deposition) - 22 Apr 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Mmps, Metalloprotease, Hydrolase, Mmp-13, Collagenase, Zinc Chelator, Hydroxamate, Hydrophobic S1', P1' Group, Calcium, Collagen Degradation, Disease Mutation, Extracellular Matrix, Glycoprotein, Metal-Binding, Polymorphism, Secreted, Zymogen
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Huang, D. Joseph-Mccarthy, F. Lovering, L. Sun, W. Wang, W. Xu, Y. Zhu, J. Cui, Y. Zhang, J. I. Levin
Structure-Based Design Of Tace Selective Inhibitors: Manipulations In The S1'-S3' Pocket.
Bioorg. Med. Chem. V. 15 6170 2007
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 22)
Info
All Hetero Components
1a: TERT-BUTYL 4-({[4-(BUT-2-YN-1-YLAM... (347a)
1b: TERT-BUTYL 4-({[4-(BUT-2-YN-1-YLAM... (347b)
1c: TERT-BUTYL 4-({[4-(BUT-2-YN-1-YLAM... (347c)
1d: TERT-BUTYL 4-({[4-(BUT-2-YN-1-YLAM... (347d)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
2e: CALCIUM ION (CAe)
2f: CALCIUM ION (CAf)
2g: CALCIUM ION (CAg)
2h: CALCIUM ION (CAh)
2i: CALCIUM ION (CAi)
2j: CALCIUM ION (CAj)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
3e: ZINC ION (ZNe)
3f: ZINC ION (ZNf)
3g: ZINC ION (ZNg)
3h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
347
4
Ligand/Ion
TERT-BUTYL 4-({[4-(BUT-2-YN-1-YLAMINO)PHENYL]SULFONYL}METHYL)-4-[(HYDROXYAMINO)CARBONYL]PIPERIDINE-1-CARBOXYLATE
2
CA
10
Ligand/Ion
CALCIUM ION
3
ZN
8
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(20, 20)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS B:197 , HIS B:201 , HIS B:207
BINDING SITE FOR RESIDUE ZN B 302
02
AC2
SOFTWARE
HIS B:147 , ASP B:149 , HIS B:162 , HIS B:175
BINDING SITE FOR RESIDUE ZN B 303
03
AC3
SOFTWARE
ASP B:154 , GLY B:155 , SER B:157 , LEU B:159 , ASP B:177 , GLU B:180
BINDING SITE FOR RESIDUE CA B 304
04
AC4
SOFTWARE
ASP B:137 , ASN B:169 , TYR B:170 , GLY B:171 , ASP B:173
BINDING SITE FOR RESIDUE CA B 305
05
AC5
SOFTWARE
HIS A:197 , HIS A:201 , HIS A:207
BINDING SITE FOR RESIDUE ZN A 302
06
AC6
SOFTWARE
HIS A:147 , ASP A:149 , HIS A:162 , HIS A:175
BINDING SITE FOR RESIDUE ZN A 303
07
AC7
SOFTWARE
ASP A:154 , GLY A:155 , SER A:157 , LEU A:159 , ASP A:177 , GLU A:180
BINDING SITE FOR RESIDUE CA A 304
08
AC8
SOFTWARE
ASP A:137 , ASN A:169 , GLY A:171 , ASP A:173
BINDING SITE FOR RESIDUE CA A 305
09
AC9
SOFTWARE
HIS C:197 , HIS C:201 , HIS C:207
BINDING SITE FOR RESIDUE ZN C 302
10
BC1
SOFTWARE
HIS C:147 , ASP C:149 , HIS C:162 , HIS C:175
BINDING SITE FOR RESIDUE ZN C 303
11
BC2
SOFTWARE
ASP C:154 , GLY C:155 , SER C:157 , LEU C:159 , ASP C:177 , GLU C:180
BINDING SITE FOR RESIDUE CA C 304
12
BC3
SOFTWARE
ASP C:137 , ASN C:169 , TYR C:170 , GLY C:171 , ASP C:173
BINDING SITE FOR RESIDUE CA C 305
13
BC4
SOFTWARE
HIS D:197 , HIS D:201 , HIS D:207
BINDING SITE FOR RESIDUE ZN D 302
14
BC5
SOFTWARE
HIS D:147 , ASP D:149 , HIS D:162 , HIS D:175
BINDING SITE FOR RESIDUE ZN D 303
15
BC6
SOFTWARE
ASP D:154 , GLY D:155 , SER D:157 , LEU D:159 , ASP D:177 , GLU D:180
BINDING SITE FOR RESIDUE CA D 304
16
BC7
SOFTWARE
ASP D:137 , ASN D:169 , TYR D:170 , GLY D:171 , ASP D:173
BINDING SITE FOR RESIDUE CA D 305
17
BC8
SOFTWARE
GLY A:158 , LEU A:160 , ALA A:161 , HIS A:197 , GLU A:198 , HIS A:201 , HIS A:207 , PRO A:217 , TYR A:219 , THR A:220 , PRO B:168 , ASN B:169
BINDING SITE FOR RESIDUE 347 A 401
18
BC9
SOFTWARE
LEU B:160 , ALA B:161 , LEU B:193 , HIS B:197 , GLU B:198 , HIS B:201 , HIS B:207 , PRO B:217 , TYR B:219 , THR B:220
BINDING SITE FOR RESIDUE 347 B 401
19
CC1
SOFTWARE
LEU C:160 , ALA C:161 , HIS C:162 , HIS C:197 , GLU C:198 , HIS C:201 , HIS C:207 , PRO C:217 , ILE C:218 , TYR C:219 , THR C:220
BINDING SITE FOR RESIDUE 347 C 401
20
CC2
SOFTWARE
PRO C:168 , ASN C:169 , GLY D:158 , LEU D:159 , LEU D:160 , ALA D:161 , HIS D:162 , HIS D:197 , GLU D:198 , HIS D:201 , HIS D:207 , PRO D:217 , ILE D:218 , TYR D:219 , THR D:220
BINDING SITE FOR RESIDUE 347 D 401
[
close Site info
]
SAPs(SNPs)/Variants
(2, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_073418 (W182G, chain A/B/C/D, )
2: VAR_063434 (H207N, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_073418
W
207
G
MMP13_HUMAN
Disease (MDST)
---
A/B/C/D
W
182
G
2
UniProt
VAR_063434
H
232
N
MMP13_HUMAN
Disease (MANDP1)
---
A/B/C/D
H
207
N
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: ZINC_PROTEASE (A:194-203,B:194-203,C:194-203,D:19...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ZINC_PROTEASE
PS00142
Neutral zinc metallopeptidases, zinc-binding region signature.
MMP13_HUMAN
219-228
4
A:194-203
B:194-203
C:194-203
D:194-203
[
close PROSITE info
]
Exons
(5, 20)
Info
All Exons
Exon 1.2 (A:79-96 | B:79-96 (gaps) | C:79-96...)
Exon 1.3 (A:96-146 | B:96-146 | C:96-146 | D...)
Exon 1.4 (A:146-188 | B:146-188 | C:146-188 ...)
Exon 1.5 (A:188-242 (gaps) | B:188-242 | C:1...)
Exon 1.6 (A:242-243 | B:242-243 | C:242-243 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1a/1.2
2: Boundary 1.2/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/1.5
5: Boundary 1.5/1.6
6: Boundary 1.6/1.7
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1a
ENST00000260302
1a
ENSE00001105391
chr11:
102826463-102826315
149
MMP13_HUMAN
1-40
40
0
-
-
1.2
ENST00000260302
2
ENSE00001105386
chr11:
102826222-102825981
242
MMP13_HUMAN
41-121
81
4
A:79-96
B:79-96 (gaps)
C:79-96 (gaps)
D:79-96 (gaps)
18
18
18
18
1.3
ENST00000260302
3
ENSE00001105401
chr11:
102825335-102825187
149
MMP13_HUMAN
121-171
51
4
A:96-146
B:96-146
C:96-146
D:96-146
51
51
51
51
1.4
ENST00000260302
4
ENSE00001105398
chr11:
102825010-102824885
126
MMP13_HUMAN
171-213
43
4
A:146-188
B:146-188
C:146-188
D:146-188
43
43
43
43
1.5
ENST00000260302
5
ENSE00001139473
chr11:
102822902-102822741
162
MMP13_HUMAN
213-267
55
4
A:188-242 (gaps)
B:188-242
C:188-242 (gaps)
D:188-242 (gaps)
55
55
55
55
1.6
ENST00000260302
6
ENSE00000930343
chr11:
102820956-102820839
118
MMP13_HUMAN
267-306
40
4
A:242-243
B:242-243
C:242-243
D:242-243
2
2
2
2
1.7
ENST00000260302
7
ENSE00000930342
chr11:
102819887-102819754
134
MMP13_HUMAN
306-351
46
0
-
-
1.8
ENST00000260302
8
ENSE00000930341
chr11:
102818779-102818620
160
MMP13_HUMAN
351-404
54
0
-
-
1.9
ENST00000260302
9
ENSE00000930340
chr11:
102816478-102816375
104
MMP13_HUMAN
404-439
36
0
-
-
1.11b
ENST00000260302
11b
ENSE00002188786
chr11:
102815095-102813724
1372
MMP13_HUMAN
439-471
33
0
-
-
[
close EXON info
]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2pjta_ (A:)
1b: SCOP_d2pjtb_ (B:)
1c: SCOP_d2pjtc_ (C:)
1d: SCOP_d2pjtd_ (D:)
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(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Zincin-like
(701)
Superfamily
:
Metalloproteases (zincins), catalytic domain
(647)
Family
:
Matrix metalloproteases, catalytic domain
(199)
Protein domain
:
Collagenase-3 (MMP-13)
(31)
Human (Homo sapiens) [TaxId: 9606]
(30)
1a
d2pjta_
A:
1b
d2pjtb_
B:
1c
d2pjtc_
C:
1d
d2pjtd_
D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2pjtB00 (B:79-243)
1b: CATH_2pjtA00 (A:79-243)
1c: CATH_2pjtD00 (D:79-243)
1d: CATH_2pjtC00 (C:79-243)
View:
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Classes
(
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(
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Architectures
(
)
(
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Collagenase (Catalytic Domain)
(236)
Homologous Superfamily
:
Collagenase (Catalytic Domain)
(234)
Human (Homo sapiens)
(153)
1a
2pjtB00
B:79-243
1b
2pjtA00
A:79-243
1c
2pjtD00
D:79-243
1d
2pjtC00
C:79-243
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Peptidase_M10_2pjtD01 (D:87-242)
1b: PFAM_Peptidase_M10_2pjtD02 (D:87-242)
1c: PFAM_Peptidase_M10_2pjtD03 (D:87-242)
1d: PFAM_Peptidase_M10_2pjtD04 (D:87-242)
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Clans
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Organisms
(
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)
Clan
:
Peptidase_MA
(251)
Family
:
Peptidase_M10
(85)
Homo sapiens (Human)
(82)
1a
Peptidase_M10-2pjtD01
D:87-242
1b
Peptidase_M10-2pjtD02
D:87-242
1c
Peptidase_M10-2pjtD03
D:87-242
1d
Peptidase_M10-2pjtD04
D:87-242
[
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]
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