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Asym. Unit
Info
Asym.Unit (66 KB)
Biol.Unit 1 (32 KB)
Biol.Unit 2 (31 KB)
Biol.Unit 3 (116 KB)
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(1)
Title
:
MMP-9 ACTIVE SITE MUTANT WITH BARBITURATE INHIBITOR
Authors
:
A. Tochowicz, W. Bode, K. Maskos, P. Goettig
Date
:
15 Feb 07 (Deposition) - 19 Jun 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: A,B (2x)
Keywords
:
Matrix Metalloproteinase, S1-Prime Pocket, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Tochowicz, K. Maskos, R. Huber, R. Oltenfreiter, V. Dive, A. Yiotakis, M. Zanda, W. Bode, P. Goettig
Crystal Structures Of Mmp-9 Complexes With Five Inhibitors: Contribution Of The Flexible Arg424 Side-Chain To Selectivity.
J. Mol. Biol. V. 371 989 2007
[
close entry info
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Hetero Components
(4, 21)
Info
All Hetero Components
1a: 5-(4-PHENOXYPHENYL)-5-(4-PYRIMIDIN... (4MRa)
1b: 5-(4-PHENOXYPHENYL)-5-(4-PYRIMIDIN... (4MRb)
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)
3a: CHLORIDE ION (CLa)
3b: CHLORIDE ION (CLb)
3c: CHLORIDE ION (CLc)
3d: CHLORIDE ION (CLd)
3e: CHLORIDE ION (CLe)
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
4MR
2
Ligand/Ion
5-(4-PHENOXYPHENYL)-5-(4-PYRIMIDIN-2-YLPIPERAZIN-1-YL)PYRIMIDINE-2,4,6(2H,3H)-TRIONE
2
CA
10
Ligand/Ion
CALCIUM ION
3
CL
5
Ligand/Ion
CHLORIDE ION
4
ZN
4
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(21, 21)
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)
21: CC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:401 , HIS A:405 , HIS A:411 , 4MR A:501
BINDING SITE FOR RESIDUE ZN A 444
02
AC2
SOFTWARE
HIS A:175 , ASP A:177 , HIS A:190 , HIS A:203
BINDING SITE FOR RESIDUE ZN A 445
03
AC3
SOFTWARE
HIS B:401 , HIS B:405 , HIS B:411 , 4MR B:502
BINDING SITE FOR RESIDUE ZN B 444
04
AC4
SOFTWARE
HIS B:175 , ASP B:177 , HIS B:190 , HIS B:203
BINDING SITE FOR RESIDUE ZN B 445
05
AC5
SOFTWARE
ASP A:182 , GLY A:183 , ASP A:185 , LEU A:187 , ASP A:205 , GLU A:208
BINDING SITE FOR RESIDUE CA A 446
06
AC6
SOFTWARE
ASP A:165 , GLY A:197 , GLN A:199 , ASP A:201 , HOH A:569 , HOH A:595
BINDING SITE FOR RESIDUE CA A 447
07
AC7
SOFTWARE
ASP A:131 , ASP A:206 , GLU A:208
BINDING SITE FOR RESIDUE CA A 448
08
AC8
SOFTWARE
SER A:211 , GLY A:213 , GLY A:215 , GLN A:391 , GLY A:392 , HOH A:503 , HOH A:584
BINDING SITE FOR RESIDUE CA A 449
09
AC9
SOFTWARE
SER A:149 , THR A:152 , HOH A:541 , HOH A:558 , HOH A:577
BINDING SITE FOR RESIDUE CA A 450
10
BC1
SOFTWARE
ASP B:182 , GLY B:183 , ASP B:185 , LEU B:187 , ASP B:205 , GLU B:208
BINDING SITE FOR RESIDUE CA B 446
11
BC2
SOFTWARE
ASP B:165 , GLY B:197 , GLN B:199 , ASP B:201
BINDING SITE FOR RESIDUE CA B 447
12
BC3
SOFTWARE
ASP B:131 , ASP B:206 , GLU B:208 , HOH B:551
BINDING SITE FOR RESIDUE CA B 448
13
BC4
SOFTWARE
LEU A:212 , SER B:211 , LEU B:212 , GLY B:213 , LYS B:214 , HOH B:550 , HOH B:568
BINDING SITE FOR RESIDUE CA B 449
14
BC5
SOFTWARE
SER B:149 , THR B:152 , HOH B:533 , HOH B:562
BINDING SITE FOR RESIDUE CA B 450
15
BC6
SOFTWARE
GLY A:213 , SER A:394
BINDING SITE FOR RESIDUE CL A 451
16
BC7
SOFTWARE
ARG A:143 , PHE A:396 , HOH B:521
BINDING SITE FOR RESIDUE CL A 452
17
BC8
SOFTWARE
HOH A:504 , GLY B:213 , SER B:394
BINDING SITE FOR RESIDUE CL B 451
18
BC9
SOFTWARE
ARG B:143 , PHE B:396
BINDING SITE FOR RESIDUE CL B 452
19
CC1
SOFTWARE
ASN A:127 , TYR A:128 , TYR B:128
BINDING SITE FOR RESIDUE CL A 453
20
CC2
SOFTWARE
LEU A:187 , LEU A:188 , ALA A:189 , HIS A:401 , GLN A:402 , HIS A:405 , HIS A:411 , LEU A:418 , TYR A:420 , PRO A:421 , MET A:422 , TYR A:423 , ARG A:424 , ZN A:444 , HOH A:521 , HOH A:570 , PRO B:421 , 4MR B:502
BINDING SITE FOR RESIDUE 4MR A 501
21
CC3
SOFTWARE
MET A:422 , 4MR A:501 , HOH A:570 , LEU B:188 , ALA B:189 , HIS B:401 , GLN B:402 , HIS B:405 , HIS B:411 , LEU B:418 , PRO B:421 , MET B:422 , TYR B:423 , ARG B:424 , ZN B:444 , HOH B:541
BINDING SITE FOR RESIDUE 4MR B 502
[
close Site info
]
SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_020054 (N127K, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_020054
N
127
K
MMP9_HUMAN
Polymorphism
3918252
A/B
N
127
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: ZINC_PROTEASE (A:398-407,B:398-407)
;
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.
MMP9_HUMAN
398-407
2
A:398-407
B:398-407
[
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]
Exons
(5, 10)
Info
All Exons
Exon 1.2 (A:110-124 | B:110-124)
Exon 1.3 (A:124-174 | B:124-174)
Exon 1.4 (A:174-215 | B:174-215)
Exon 1.7 (A:391-392 | B:391-392)
Exon 1.8 (A:392-443 | B:392-443)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1/1.2
2: Boundary 1.2/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/1.5
5: Boundary 1.6/1.7
6: Boundary 1.7/1.8
7: Boundary 1.8/1.9
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENST00000372330
1
ENSE00001457585
chr20:
44637547-44637703
157
MMP9_HUMAN
1-46
46
0
-
-
1.2
ENST00000372330
2
ENSE00000662462
chr20:
44638505-44638737
233
MMP9_HUMAN
47-124
78
2
A:110-124
B:110-124
15
15
1.3
ENST00000372330
3
ENSE00000845116
chr20:
44639122-44639270
149
MMP9_HUMAN
124-174
51
2
A:124-174
B:124-174
51
51
1.4
ENST00000372330
4
ENSE00000845117
chr20:
44639561-44639689
129
MMP9_HUMAN
174-217
44
2
A:174-215
B:174-215
42
42
1.5
ENST00000372330
5
ENSE00000845118
chr20:
44639782-44639955
174
MMP9_HUMAN
217-275
59
0
-
-
1.6
ENST00000372330
6
ENSE00000845119
chr20:
44640213-44640386
174
MMP9_HUMAN
275-333
59
0
-
-
1.7
ENST00000372330
7
ENSE00000845120
chr20:
44640776-44640952
177
MMP9_HUMAN
333-392
60
2
A:391-392
B:391-392
2
2
1.8
ENST00000372330
8
ENSE00000845121
chr20:
44641066-44641221
156
MMP9_HUMAN
392-444
53
2
A:392-443
B:392-443
52
52
1.9
ENST00000372330
9
ENSE00000845122
chr20:
44641894-44642173
280
MMP9_HUMAN
444-537
94
0
-
-
1.10
ENST00000372330
10
ENSE00000845123
chr20:
44642296-44642435
140
MMP9_HUMAN
537-584
48
0
-
-
1.11
ENST00000372330
11
ENSE00000845124
chr20:
44642763-44642913
151
MMP9_HUMAN
584-634
51
0
-
-
1.12
ENST00000372330
12
ENSE00000845125
chr20:
44643010-44643113
104
MMP9_HUMAN
634-669
36
0
-
-
1.13
ENST00000372330
13
ENSE00001457551
chr20:
44644889-44645200
312
MMP9_HUMAN
669-707
39
0
-
-
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2ovxa_ (A:)
1b: SCOP_d2ovxb_ (B:)
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Classes
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Folds
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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
:
Gelatinase B (MMP-9)
(13)
Human (Homo sapiens) [TaxId: 9606]
(13)
1a
d2ovxa_
A:
1b
d2ovxb_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2ovxA00 (A:110-443)
1b: CATH_2ovxB00 (B:110-443)
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Homologous Superfamilies
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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
2ovxA00
A:110-443
1b
2ovxB00
B:110-443
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Peptidase_M10_2ovxB01 (B:115-443)
1b: PFAM_Peptidase_M10_2ovxB02 (B:115-443)
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Clans
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(
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Families
(
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(
)
Organisms
(
)
(
)
Clan
:
Peptidase_MA
(251)
Family
:
Peptidase_M10
(85)
Homo sapiens (Human)
(82)
1a
Peptidase_M10-2ovxB01
B:115-443
1b
Peptidase_M10-2ovxB02
B:115-443
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