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3KRY
Biol. Unit 5
Info
Asym.Unit (128 KB)
Biol.Unit 1 (33 KB)
Biol.Unit 2 (33 KB)
Biol.Unit 3 (33 KB)
Biol.Unit 4 (33 KB)
Biol.Unit 5 (119 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF MMP-13 IN COMPLEX WITH SC-78080
Authors
:
J. R. Kiefer, J. M. Williams, D. P. Becker
Date
:
19 Nov 09 (Deposition) - 06 Oct 10 (Release) - 24 Jun 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
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)
Biol. Unit 5: A,B,C,D (1x)
Keywords
:
Collagenase, Collagenase-3, Mmp-13, Collagen Degradation, Disease Mutation, Disulfide Bond, Extracellular Matrix, Glycoprotein, Hydrolase, Metal-Binding, Metalloprotease, Protease, Secreted
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. P. Becker, T. E. Barta, L. J. Bedell, T. L. Boehm, B. R. Bond, J. Carroll, C. P. Carron, G. A. Decrescenzo, A. M. Easton, J. N. Freskos C. L. Funckes-Shippy, M. Heron, S. Hockerman, C. P. Howard, J. R. Kiefer, M. H. Li, K. J. Mathis, J. J. Mcdonald, P. P. Mehta, G. E. Munie, T. Sunyer, C. A. Swearingen, C. I. Villamil, D. Welsch, J. M. Williams, Y. Yu, J. Yao
Orally-Active Mmp-1 Sparing Alpha-Tetrahydropyranyl And Alpha-Piperidinyl Sulfone Matrix Metalloproteinase (Mmp) Inhibitors With Efficacy In Cancer, Arthritis, And Cardiovascular Disease
J. Med. Chem. V. 53 6653 2010
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Hetero Components
(0, 0)
Info
All Hetero Components
1a: 1-(2-METHOXYETHYL)-N-OXO-4-({4-[4-... (3KRa)
1b: 1-(2-METHOXYETHYL)-N-OXO-4-({4-[4-... (3KRb)
1c: 1-(2-METHOXYETHYL)-N-OXO-4-({4-[4-... (3KRc)
1d: 1-(2-METHOXYETHYL)-N-OXO-4-({4-[4-... (3KRd)
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)
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)
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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 A:172 , ASP A:174 , HIS A:187 , HIS A:200
BINDING SITE FOR RESIDUE ZN A 1998
02
AC2
SOFTWARE
HIS A:222 , HIS A:226 , HIS A:232 , 3KR A:1800
BINDING SITE FOR RESIDUE ZN A 1999
03
AC3
SOFTWARE
HOH A:14 , ASP A:162 , ASN A:194 , GLY A:196 , ASP A:198 , HOH A:303
BINDING SITE FOR RESIDUE CA A 1996
04
AC4
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 1997
05
AC5
SOFTWARE
HOH A:33 , LEU A:184 , LEU A:185 , ALA A:186 , VAL A:219 , HIS A:222 , GLU A:223 , HIS A:226 , HIS A:232 , ALA A:238 , LEU A:239 , PHE A:241 , PRO A:242 , ILE A:243 , TYR A:244 , THR A:245 , HOH A:299 , HOH A:328 , ZN A:1999
BINDING SITE FOR RESIDUE 3KR A 1800
06
AC6
SOFTWARE
HIS B:172 , ASP B:174 , HIS B:187 , HIS B:200
BINDING SITE FOR RESIDUE ZN B 2998
07
AC7
SOFTWARE
HIS B:222 , HIS B:226 , HIS B:232 , 3KR B:2800
BINDING SITE FOR RESIDUE ZN B 2999
08
AC8
SOFTWARE
HOH B:96 , ASP B:162 , ASN B:194 , GLY B:196 , ASP B:198 , HOH B:295
BINDING SITE FOR RESIDUE CA B 2996
09
AC9
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 2997
10
BC1
SOFTWARE
LEU B:184 , LEU B:185 , ALA B:186 , LEU B:218 , VAL B:219 , 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 , HOH B:302 , HOH B:419 , HOH B:519 , ZN B:2999
BINDING SITE FOR RESIDUE 3KR B 2800
11
BC2
SOFTWARE
HIS C:172 , ASP C:174 , HIS C:187 , HIS C:200
BINDING SITE FOR RESIDUE ZN C 3998
12
BC3
SOFTWARE
HIS C:222 , HIS C:226 , HIS C:232 , 3KR C:3800
BINDING SITE FOR RESIDUE ZN C 3999
13
BC4
SOFTWARE
ASP C:162 , ASN C:194 , GLY C:196 , ASP C:198 , HOH C:283 , HOH C:438
BINDING SITE FOR RESIDUE CA C 3996
14
BC5
SOFTWARE
ASP C:179 , GLY C:180 , SER C:182 , LEU C:184 , ASP C:202 , GLU C:205
BINDING SITE FOR RESIDUE CA C 3997
15
BC6
SOFTWARE
GLY C:183 , LEU C:184 , LEU C:185 , ALA C:186 , LEU C:218 , VAL C:219 , HIS C:222 , GLU C:223 , HIS C:226 , HIS C:232 , LEU C:239 , PHE C:241 , PRO C:242 , ILE C:243 , TYR C:244 , THR C:245 , THR C:247 , HOH C:368 , HOH C:483 , ZN C:3999
BINDING SITE FOR RESIDUE 3KR C 3800
16
BC7
SOFTWARE
HIS D:172 , ASP D:174 , HIS D:187 , HIS D:200
BINDING SITE FOR RESIDUE ZN D 4998
17
BC8
SOFTWARE
HIS D:222 , HIS D:226 , HIS D:232 , 3KR D:4800
BINDING SITE FOR RESIDUE ZN D 4999
18
BC9
SOFTWARE
ASP D:162 , ASN D:194 , GLY D:196 , ASP D:198 , HOH D:286 , HOH D:305
BINDING SITE FOR RESIDUE CA D 4996
19
CC1
SOFTWARE
ASP D:179 , GLY D:180 , SER D:182 , LEU D:184 , ASP D:202 , GLU D:205
BINDING SITE FOR RESIDUE CA D 4997
20
CC2
SOFTWARE
GLY D:183 , LEU D:184 , LEU D:185 , ALA D:186 , LEU D:218 , VAL D:219 , HIS D:222 , GLU D:223 , HIS D:226 , HIS D:232 , LEU D:239 , PHE D:241 , PRO D:242 , ILE D:243 , TYR D:244 , THR D:245 , THR D:247 , ZN D:4999
BINDING SITE FOR RESIDUE 3KR D 4800
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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/C/D, )
2: VAR_063434 (H232N, chain A/B/C/D, )
View:
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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
207
G
2
UniProt
VAR_063434
H
232
N
MMP13_HUMAN
Disease (MANDP1)
---
A/B/C/D
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,C:219-228,D:21...)
;
View:
Select:
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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
C:219-228
D: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_d3krya_ (A:)
1b: SCOP_d3kryb_ (B:)
1c: SCOP_d3kryc_ (C:)
1d: SCOP_d3kryd_ (D:)
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Organisms
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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
d3krya_
A:
1b
d3kryb_
B:
1c
d3kryc_
C:
1d
d3kryd_
D:
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Peptidase_M10_3kryD01 (D:112-267)
1b: PFAM_Peptidase_M10_3kryD02 (D:112-267)
1c: PFAM_Peptidase_M10_3kryD03 (D:112-267)
1d: PFAM_Peptidase_M10_3kryD04 (D:112-267)
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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_M10-3kryD01
D:112-267
1b
Peptidase_M10-3kryD02
D:112-267
1c
Peptidase_M10-3kryD03
D:112-267
1d
Peptidase_M10-3kryD04
D:112-267
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