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1ZTQ
Biol. Unit 4
Info
Asym.Unit (125 KB)
Biol.Unit 1 (33 KB)
Biol.Unit 2 (33 KB)
Biol.Unit 3 (32 KB)
Biol.Unit 4 (32 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF MMP-13 COMPLEXED WITH WAY-033
Authors
:
J. Wu, T. S. Rush Iii, R. Hotchandani, X. Du, M. Geck, E. Collins, Z. B. Xu, J. Skotnicki, J. I. Levin, F. Lovering
Date
:
27 May 05 (Deposition) - 30 May 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
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
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Wu, T. S. Rush Iii, R. Hotchandani, X. Du, M. Geck, E. Collins, Z. B. Xu, J. Skotnicki, J. I. Levin, F. E. Lovering
Identification Of Potent And Selective Mmp-13 Inhibitors
Bioorg. Med. Chem. Lett. V. 15 4105 2005
(for further references see the
PDB file header
)
[
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: N-({4'-[(1-BENZOFURAN-2-YLCARBONYL... (033a)
1b: N-({4'-[(1-BENZOFURAN-2-YLCARBONYL... (033b)
1c: N-({4'-[(1-BENZOFURAN-2-YLCARBONYL... (033c)
1d: N-({4'-[(1-BENZOFURAN-2-YLCARBONYL... (033d)
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)
2k: CALCIUM ION (CAk)
2l: CALCIUM ION (CAl)
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
033
1
Ligand/Ion
N-({4'-[(1-BENZOFURAN-2-YLCARBONYL)AMINO]-1,1'-BIPHENYL-4-YL}SULFONYL)-L-VALINE
2
CA
-1
Ligand/Ion
CALCIUM ION
3
ZN
-1
Ligand/Ion
ZINC ION
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Sites
(6, 6)
Info
All Sites
1: BC7 (SOFTWARE)
2: BC8 (SOFTWARE)
3: BC9 (SOFTWARE)
4: CC1 (SOFTWARE)
5: CC2 (SOFTWARE)
6: CC6 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
BC7
SOFTWARE
HIS D:197 , HIS D:201 , HIS D:207 , 033 D:604
BINDING SITE FOR RESIDUE ZN D 556
2
BC8
SOFTWARE
HIS D:147 , ASP D:149 , HIS D:162 , HIS D:175
BINDING SITE FOR RESIDUE ZN D 557
3
BC9
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 569
4
CC1
SOFTWARE
ASP D:137 , ASN D:169 , GLY D:171 , ASP D:173 , HOH D:711 , HOH D:712
BINDING SITE FOR RESIDUE CA D 570
5
CC2
SOFTWARE
HOH A:656 , ASP D:103 , ASP D:178 , GLU D:180
BINDING SITE FOR RESIDUE CA D 571
6
CC6
SOFTWARE
LEU D:159 , LEU D:160 , ALA D:161 , LEU D:193 , HIS D:197 , GLU D:198 , HIS D:201 , HIS D:207 , GLY D:212 , LEU D:214 , PHE D:216 , PRO D:217 , ILE D:218 , TYR D:219 , ZN D:556 , HOH D:654 , HOH D:683
BINDING SITE FOR RESIDUE 033 D 604
[
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SAPs(SNPs)/Variants
(2, 2)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_073418 (W182G, chain D, )
2: VAR_063434 (H207N, chain 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)
---
D
W
182
G
2
UniProt
VAR_063434
H
232
N
MMP13_HUMAN
Disease (MANDP1)
---
D
H
207
N
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: ZINC_PROTEASE (D:194-203)
;
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
1
-
-
-
D:194-203
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Exons
(0, 0)
Info
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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, 4)
Info
All SCOP Domains
1a: SCOP_d1ztqa_ (A:)
1b: SCOP_d1ztqb_ (B:)
1c: SCOP_d1ztqc_ (C:)
1d: SCOP_d1ztqd_ (D:)
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)
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)
(
)
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
d1ztqa_
A:
1b
d1ztqb_
B:
1c
d1ztqc_
C:
1d
d1ztqd_
D:
[
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1ztqA00 (A:79-243)
1b: CATH_1ztqB00 (B:79-243)
1c: CATH_1ztqD00 (D:79-243)
1d: CATH_1ztqC00 (C:79-243)
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)
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(
)
(
)
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
1ztqA00
A:79-243
1b
1ztqB00
B:79-243
1c
1ztqD00
D:79-243
1d
1ztqC00
C:79-243
[
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Peptidase_M10_1ztqD01 (D:87-242)
1b: PFAM_Peptidase_M10_1ztqD02 (D:87-242)
1c: PFAM_Peptidase_M10_1ztqD03 (D:87-242)
1d: PFAM_Peptidase_M10_1ztqD04 (D:87-242)
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Clans
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(
)
Organisms
(
)
(
)
Clan
:
Peptidase_MA
(251)
Family
:
Peptidase_M10
(85)
Homo sapiens (Human)
(82)
1a
Peptidase_M10-1ztqD01
D:87-242
1b
Peptidase_M10-1ztqD02
D:87-242
1c
Peptidase_M10-1ztqD03
D:87-242
1d
Peptidase_M10-1ztqD04
D:87-242
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Chain D
Asymmetric Unit 1
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