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1YOU
Biol. Unit 3
Info
Asym.Unit (63 KB)
Biol.Unit 1 (30 KB)
Biol.Unit 2 (30 KB)
Biol.Unit 3 (111 KB)
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Title
:
CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF MMP-13 COMPLEXED WITH A POTENT PYRIMIDINETRIONE INHIBITOR
Authors
:
J. Pandit
Date
:
28 Jan 05 (Deposition) - 15 Mar 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: A,B (2x)
Keywords
:
Hydrolase, Metalloprotease
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. A. Blagg, M. C. Noe, L. A. Wolf-Gouveia, L. A. Reiter, E. R. Laird, S. P. Chang, D. E. Danley, J. T. Downs, N. C. Elliott, J. D. Eskra, R. J. Griffiths, J. R. Hardink, A. I. Haugeto, C. S. Jones, J. L. Liras, L. L. Lopresti-Morrow, P. G. Mitchell, J. Pandit, R. P. Robinson, C. Subramanyam, M. L. Vaughn-Bowser, S. A. Yocum
Potent Pyrimidinetrione-Based Inhibitors Of Mmp-13 With Enhanced Selectivity Over Mmp-14.
Bioorg. Med. Chem. Lett. V. 15 1807 2005
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Hetero Components
(2, 10)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: 5-(2-ETHOXYETHYL)-5-[4-(4-FLUOROPH... (PFDa)
2b: 5-(2-ETHOXYETHYL)-5-[4-(4-FLUOROPH... (PFDb)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
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
PFD
4
Ligand/Ion
5-(2-ETHOXYETHYL)-5-[4-(4-FLUOROPHENOXY)PHENOXY]PYRIMIDINE-2,4,6(1H,3H,5H)-TRIONE
3
SO4
6
Ligand/Ion
SULFATE ION
4
ZN
-1
Ligand/Ion
ZINC ION
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Sites
(11, 11)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:222 , HIS A:226 , HIS A:232 , PFD A:998
BINDING SITE FOR RESIDUE ZN A 301
02
AC2
SOFTWARE
HIS A:172 , ASP A:174 , HIS A:187 , HIS A:200
BINDING SITE FOR RESIDUE ZN A 302
03
AC3
SOFTWARE
HIS B:222 , HIS B:226 , HIS B:232 , PFD B:999
BINDING SITE FOR RESIDUE ZN B 303
04
AC4
SOFTWARE
HIS B:172 , ASP B:174 , HIS B:187 , HIS B:200
BINDING SITE FOR RESIDUE ZN B 304
05
AC5
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 401
06
AC6
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 403
07
AC7
SOFTWARE
THR A:130 , HIS A:131 , THR B:130 , HIS B:131
BINDING SITE FOR RESIDUE SO4 A 501
08
AC8
SOFTWARE
LYS A:115 , MET A:116 , ASN A:117
BINDING SITE FOR RESIDUE SO4 A 502
09
AC9
SOFTWARE
LYS B:115 , MET B:116 , ASN B:117 , LYS B:234
BINDING SITE FOR RESIDUE SO4 B 503
10
BC1
SOFTWARE
LEU A:184 , LEU A:185 , ALA A:186 , 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 , ZN A:301
BINDING SITE FOR RESIDUE PFD A 998
11
BC2
SOFTWARE
LEU B:184 , LEU B:185 , ALA B:186 , VAL B:219 , HIS B:222 , GLU B:223 , HIS B:226 , HIS B:232 , LEU B:239 , PHE B:241 , PRO B:242 , ILE B:243 , TYR B:244 , THR B:245 , ZN B:303
BINDING SITE FOR RESIDUE PFD B 999
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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_d1youa_ (A:)
1b: SCOP_d1youb_ (B:)
View:
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Classes
(
)
(
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(
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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
d1youa_
A:
1b
d1youb_
B:
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1youA00 (A:104-271)
1b: CATH_1youB00 (B:104-268)
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)
Organisms
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)
(
)
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
1youA00
A:104-271
1b
1youB00
B:104-268
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Peptidase_M10_1youB01 (B:112-267)
1b: PFAM_Peptidase_M10_1youB02 (B:112-267)
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Clans
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)
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(
)
Organisms
(
)
(
)
Clan
:
Peptidase_MA
(251)
Family
:
Peptidase_M10
(85)
Homo sapiens (Human)
(82)
1a
Peptidase_M10-1youB01
B:112-267
1b
Peptidase_M10-1youB02
B:112-267
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (63 KB)
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Biol.Unit 1 (30 KB)
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Biol.Unit 2 (30 KB)
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Biol.Unit 3 (111 KB)
Header - Biol.Unit 3
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