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Biol. Unit 1
Info
Asym.Unit (176 KB)
Biol.Unit 1 (334 KB)
Biol.Unit 2 (168 KB)
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(1)
Title
:
MMP-13 COMPLEXED WITH 2-NAPTHYLSULFONAMIDE HYDROXAMIC ACID INHIBITOR
Authors
:
K. L. Clark, R. Kulathila
Date
:
10 Aug 11 (Deposition) - 19 Oct 11 (Release) - 26 Oct 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Biol. Unit 2: A,B (1x)
Keywords
:
Metallo-Enzyme, Carboxylate Inhibitor, Collagen Degradation, Extracellular Matrix, Hydrolase, Metal-Binding, Metalloprotease
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. A. Tommasi, S. Weiler, L. W. Mcquire, O. Rogel, M. Chambers, K. L. Clark, J. Doughty, J. Fang, V. Ganu, J. Grob, R. Goldberg, R. Goldstein, S. Lavoie, R. Kulathila, W. Macchia, R. Melton, C. Springer, M. Walker, J. Zhang, L. Zhu, M. Shultz
Potent And Selective 2-Naphthylsulfonamide Substituted Hydroxamic Acid Inhibitors Of Matrix Metalloproteinase-13.
Bioorg. Med. Chem. Lett. V. 21 6440 2011
[
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Hetero Components
(2, 14)
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)
2a: N-HYDROXY-N^2^-(3-METHYLBUTYL)-N^2... (E41a)
2b: N-HYDROXY-N^2^-(3-METHYLBUTYL)-N^2... (E41b)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
4c: ZINC ION (ZNc)
4d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
E41
4
Ligand/Ion
N-HYDROXY-N^2^-(3-METHYLBUTYL)-N^2^-(NAPHTHALEN-2-YLSULFONYL)-D-VALINAMIDE
3
GOL
10
Ligand/Ion
GLYCEROL
4
ZN
-1
Ligand/Ion
ZINC ION
[
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Sites
(18, 18)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:222 , HIS A:226 , HIS A:232 , E41 A:401
BINDING SITE FOR RESIDUE ZN A 300
02
AC2
SOFTWARE
HIS A:172 , ASP A:174 , HIS A:187 , HIS A:200
BINDING SITE FOR RESIDUE ZN A 301
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 302
04
AC4
SOFTWARE
ASP A:128 , ASP A:203 , GLU A:205 , HOH A:2036 , HOH A:2038
BINDING SITE FOR RESIDUE CA A 303
05
AC5
SOFTWARE
ASP A:162 , ASN A:194 , GLY A:196 , ASP A:198 , HOH A:2104 , HOH A:2106
BINDING SITE FOR RESIDUE CA A 304
06
AC6
SOFTWARE
SER A:146 , THR A:149 , HOH A:2061 , HOH A:2063 , HOH A:2070 , HOH A:2073
BINDING SITE FOR RESIDUE CA A 305
07
AC7
SOFTWARE
LEU A:184 , LEU A:185 , ALA A:186 , HIS A:222 , GLU A:223 , HIS A:226 , HIS A:232 , PRO A:242 , ILE A:243 , TYR A:244 , ZN A:300 , HOH A:2142
BINDING SITE FOR RESIDUE E41 A 401
08
AC8
SOFTWARE
LEU A:239 , ILE A:243 , TYR A:244 , THR A:245 , THR A:247 , HOH A:2183 , HOH A:2184
BINDING SITE FOR RESIDUE GOL A1273
09
AC9
SOFTWARE
HIS B:222 , HIS B:226 , HIS B:232 , E41 B:401
BINDING SITE FOR RESIDUE ZN B 300
10
BC1
SOFTWARE
HIS B:172 , ASP B:174 , HIS B:187 , HIS B:200
BINDING SITE FOR RESIDUE ZN B 301
11
BC2
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 302
12
BC3
SOFTWARE
ASP B:128 , ASP B:203 , GLU B:205 , HOH B:2035 , HOH B:2036
BINDING SITE FOR RESIDUE CA B 303
13
BC4
SOFTWARE
ASP B:162 , ASN B:194 , GLY B:196 , ASP B:198 , HOH B:2094 , HOH B:2095
BINDING SITE FOR RESIDUE CA B 304
14
BC5
SOFTWARE
LEU B:184 , LEU B:185 , ALA B:186 , HIS B:222 , GLU B:223 , HIS B:226 , HIS B:232 , PRO B:242 , ILE B:243 , TYR B:244 , ZN B:300 , GOL B:1273 , HOH B:2138
BINDING SITE FOR RESIDUE E41 B 401
15
BC6
SOFTWARE
ASP A:179 , GLY A:180 , PRO A:181 , GLU B:205 , THR B:206 , TYR B:214
BINDING SITE FOR RESIDUE GOL B1270
16
BC7
SOFTWARE
HIS A:172 , GLY B:168 , ILE B:169 , GLU B:171 , HOH B:2107 , HOH B:2119
BINDING SITE FOR RESIDUE GOL B1271
17
BC8
SOFTWARE
LEU B:218 , LEU B:239 , ILE B:243 , TYR B:244 , THR B:245 , HOH B:2173 , HOH B:2174 , HOH B:2178 , HOH B:2179
BINDING SITE FOR RESIDUE GOL B1272
18
BC9
SOFTWARE
GLY B:183 , TYR B:214 , ILE B:243 , TYR B:244 , E41 B:401 , HOH B:2177
BINDING SITE FOR RESIDUE GOL B1273
[
close Site info
]
SAPs(SNPs)/Variants
(2, 8)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_073418 (W207G, chain A/B, )
2: VAR_063434 (H232N, chain A/B, )
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
W
207
G
2
UniProt
VAR_063434
H
232
N
MMP13_HUMAN
Disease (MANDP1)
---
A/B
H
232
N
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: ZINC_PROTEASE (A:219-228,B:219-228)
;
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:219-228
B:219-228
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3zxha_ (A:)
1b: SCOP_d3zxhb_ (B:)
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Classes
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(
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Protein Domains
(
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(
)
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
d3zxha_
A:
1b
d3zxhb_
B:
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
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Pfam Domains
(0, 0)
Info
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Label:
Sorry, no Info available
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Asymmetric Unit 1
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Asym.Unit (176 KB)
Header - Asym.Unit
Biol.Unit 1 (334 KB)
Header - Biol.Unit 1
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Header - Biol.Unit 2
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