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3LJZ
Biol. Unit 1
Info
Asym.Unit (238 KB)
Biol.Unit 1 (60 KB)
Biol.Unit 2 (61 KB)
Biol.Unit 3 (60 KB)
Biol.Unit 4 (61 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN MMP-13 COMPLEXED WITH AN AMINO-2-INDANOL COMPOUND
Authors
:
H. -S. Shieh, J. R. Kiefer
Date
:
26 Jan 10 (Deposition) - 02 Feb 11 (Release) - 06 Apr 11 (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
:
Mmp-13 Inhibitor; Zinc Chelating Agent; S1' Pocket, Collagen Degradation, Disease Mutation, Disulfide Bond, Extracellular Matrix, Glycoprotein, Hydrolase, Metal-Binding, Metalloprotease, Protease, Secreted, Zymogen, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. S. Shieh, A. G. Tomasselli, K. J. Mathis, M. E. Schnute, S. S. Woodard N. Caspers, J. M. Williams, J. R. Kiefer, G. Munie, A. Wittwer, A. M. Malfait, M. D. Tortorella
Structure Analysis Reveals The Flexibility Of The Adamts-5 Active Site.
Protein Sci. V. 20 735 2011
[
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Hetero Components
(2, 3)
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)
2a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
2b: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEb)
2c: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEc)
2d: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEd)
3a: (2R)-2-[4-(1,3-BENZODIOXOL-5-YL)BE... (LA3a)
3b: (2R)-2-[4-(1,3-BENZODIOXOL-5-YL)BE... (LA3b)
3c: (2R)-2-[4-(1,3-BENZODIOXOL-5-YL)BE... (LA3c)
3d: (2R)-2-[4-(1,3-BENZODIOXOL-5-YL)BE... (LA3d)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
4g: SULFATE ION (SO4g)
4h: SULFATE ION (SO4h)
4i: SULFATE ION (SO4i)
5a: ZINC ION (ZNa)
5b: ZINC ION (ZNb)
5c: ZINC ION (ZNc)
5d: ZINC ION (ZNd)
5e: ZINC ION (ZNe)
5f: ZINC ION (ZNf)
5g: ZINC ION (ZNg)
5h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
EPE
-1
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3
LA3
1
Ligand/Ion
(2R)-2-[4-(1,3-BENZODIOXOL-5-YL)BENZYL]-N~4~-HYDROXY-N~1~-[(1S,2R)-2-HYDROXY-2,3-DIHYDRO-1H-INDEN-1-YL]BUTANEDIAMIDE
4
SO4
2
Ligand/Ion
SULFATE ION
5
ZN
-1
Ligand/Ion
ZINC ION
[
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Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: BC5 (SOFTWARE)
9: BC6 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ALA A:161 , ASP A:162 , ASN A:194 , GLY A:196 , ASP A:198 , HOH A:280 , HOH A:340
BINDING SITE FOR RESIDUE CA A 996
2
AC2
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 997
3
AC3
SOFTWARE
HIS A:172 , ASP A:174 , HIS A:187 , HIS A:200
BINDING SITE FOR RESIDUE ZN A 998
4
AC4
SOFTWARE
HIS A:222 , HIS A:226 , HIS A:232 , LA3 A:801
BINDING SITE FOR RESIDUE ZN A 999
5
AC5
SOFTWARE
HOH A:43 , TYR A:120 , LYS A:139 , ARG A:155
BINDING SITE FOR RESIDUE SO4 A 1
6
AC6
SOFTWARE
LYS A:115 , MET A:116 , ASN A:117
BINDING SITE FOR RESIDUE SO4 A 5
7
AC7
SOFTWARE
LEU A:184 , LEU A:185 , ALA A:186 , LEU A:218 , HIS A:222 , GLU A:223 , HIS A:226 , HIS A:232 , LEU A:239 , PHE A:241 , PRO A:242 , ILE A:243 , TYR A:244 , THR A:245 , HOH A:291 , HOH A:292 , ZN A:999
BINDING SITE FOR RESIDUE LA3 A 801
8
BC5
SOFTWARE
PRO A:236 , LYS B:115 , MET B:116 , ASN B:117 , HOH B:307 , HOH B:312
BINDING SITE FOR RESIDUE SO4 B 6
9
BC6
SOFTWARE
HOH A:98 , HOH B:4 , GLY B:183 , LEU B:184 , LEU B:185 , ALA B:186 , LEU B:218 , HIS B:222 , GLU B:223 , HIS B:226 , HIS B:232 , ALA B:238 , LEU B:239 , PHE B:241 , PRO B:242 , ILE B:243 , TYR B:244 , THR B:245 , THR B:247 , ZN B:999
BINDING SITE FOR RESIDUE LA3 B 802
[
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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 (W207G, chain A, )
2: VAR_063434 (H232N, chain A, )
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
W
207
G
2
UniProt
VAR_063434
H
232
N
MMP13_HUMAN
Disease (MANDP1)
---
A
H
232
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 (A: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
1
A: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, 4)
Info
All SCOP Domains
1a: SCOP_d3ljza_ (A:)
1b: SCOP_d3ljzb_ (B:)
1c: SCOP_d3ljzc_ (C:)
1d: SCOP_d3ljzd_ (D:)
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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
d3ljza_
A:
1b
d3ljzb_
B:
1c
d3ljzc_
C:
1d
d3ljzd_
D:
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Peptidase_M10_3ljzD01 (D:112-267)
1b: PFAM_Peptidase_M10_3ljzD02 (D:112-267)
1c: PFAM_Peptidase_M10_3ljzD03 (D:112-267)
1d: PFAM_Peptidase_M10_3ljzD04 (D:112-267)
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Clans
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(
)
Organisms
(
)
(
)
Clan
:
Peptidase_MA
(251)
Family
:
Peptidase_M10
(85)
Homo sapiens (Human)
(82)
1a
Peptidase_M10-3ljzD01
D:112-267
1b
Peptidase_M10-3ljzD02
D:112-267
1c
Peptidase_M10-3ljzD03
D:112-267
1d
Peptidase_M10-3ljzD04
D:112-267
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Chain A
Asymmetric Unit 1
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Asym.Unit (238 KB)
Header - Asym.Unit
Biol.Unit 1 (60 KB)
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Biol.Unit 3 (60 KB)
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