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1L6J
Asym. Unit
Info
Asym.Unit (75 KB)
Biol.Unit 1 (70 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN MATRIX METALLOPROTEINASE MMP9 (GELATINASE B).
Authors
:
P. A. Elkins, Y. S. Ho, W. W. Smith, C. A. Janson, K. J. D'Alessio, M. S. Mcqueney, M. D. Cummings, A. M. Romanic
Date
:
11 Mar 02 (Deposition) - 03 Jul 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Twisted Beta Sheet Flanked By Helices, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. A. Elkins, Y. S. Ho, W. W. Smith, C. A. Janson, K. J. D'Alessio, M. S. Mcqueney, M. D. Cummings, A. M. Romanic
Structure Of The C-Terminally Truncated Human Prommp9, A Gelatin-Binding Matrix Metalloproteinase.
Acta Crystallogr. , Sect. D V. 58 1182 2002
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 5)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
3
Ligand/Ion
CALCIUM ION
2
ZN
2
Ligand/Ion
ZINC ION
[
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]
Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS A:99 , HIS A:401 , HIS A:405 , HIS A:411
BINDING SITE FOR RESIDUE ZN A 500
2
AC2
SOFTWARE
HIS A:175 , ASP A:177 , HIS A:190 , HIS A:203
BINDING SITE FOR RESIDUE ZN A 501
3
AC3
SOFTWARE
ASP A:182 , GLY A:183 , GLY A:186 , LEU A:187 , ASP A:205 , GLU A:208
BINDING SITE FOR RESIDUE CA A 502
4
AC4
SOFTWARE
ASP A:131 , ASP A:206 , GLU A:208 , HOH A:1054
BINDING SITE FOR RESIDUE CA A 503
5
AC5
SOFTWARE
ALA A:164 , ASP A:165 , GLY A:197 , GLN A:199 , ASP A:201 , HOH A:1052 , HOH A:1174
BINDING SITE FOR RESIDUE CA A 504
[
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]
SAPs(SNPs)/Variants
(5, 5)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_037004 (N38S, chain A, )
2: VAR_013781 (E82K, chain A, )
3: VAR_020054 (N127K, chain A, )
4: VAR_025165 (R239H, chain A, )
5: VAR_013782 (R279R, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_037004
N
38
S
MMP9_HUMAN
Polymorphism
41427445
A
N
38
S
2
UniProt
VAR_013781
E
82
K
MMP9_HUMAN
Polymorphism
1805089
A
E
82
K
3
UniProt
VAR_020054
N
127
K
MMP9_HUMAN
Polymorphism
3918252
A
N
127
K
4
UniProt
VAR_025165
R
239
H
MMP9_HUMAN
Polymorphism
28763886
A
R
239
H
5
UniProt
VAR_013782
Q
279
R
MMP9_HUMAN
Polymorphism
17576
A
R
279
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(4, 8)
Info
All PROSITE Patterns/Profiles
1: CYSTEINE_SWITCH (A:97-104)
2: FN2_2 (A:225-273|A:283-331|A:342-390)
3: FN2_1 (A:230-271|A:288-329|A:347-388)
4: ZINC_PROTEASE (A:398-407)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CYSTEINE_SWITCH
PS00546
Matrixins cysteine switch.
MMP9_HUMAN
97-104
1
A:97-104
2
FN2_2
PS51092
Fibronectin type-II collagen-binding domain profile.
MMP9_HUMAN
225-273
283-331
342-390
3
A:225-273
A:283-331
A:342-390
3
FN2_1
PS00023
Fibronectin type-II collagen-binding domain signature.
MMP9_HUMAN
230-271
288-329
347-388
3
A:230-271
A:288-329
A:347-388
4
ZINC_PROTEASE
PS00142
Neutral zinc metallopeptidases, zinc-binding region signature.
MMP9_HUMAN
398-407
1
A:398-407
[
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]
Exons
(9, 9)
Info
All Exons
Exon 1.1 (A:29-46)
Exon 1.2 (A:47-124 (gaps))
Exon 1.3 (A:124-174)
Exon 1.4 (A:174-217)
Exon 1.5 (A:217-275)
Exon 1.6 (A:275-333)
Exon 1.7 (A:333-392)
Exon 1.8 (A:392-444)
Exon 1.9 (A:444-444)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1
02: Boundary 1.1/1.2
03: Boundary 1.2/1.3
04: Boundary 1.3/1.4
05: Boundary 1.4/1.5
06: Boundary 1.5/1.6
07: Boundary 1.6/1.7
08: Boundary 1.7/1.8
09: Boundary 1.8/1.9
10: Boundary 1.9/1.10
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
1
A:29-46
18
1.2
ENST00000372330
2
ENSE00000662462
chr20:
44638505-44638737
233
MMP9_HUMAN
47-124
78
1
A:47-124 (gaps)
78
1.3
ENST00000372330
3
ENSE00000845116
chr20:
44639122-44639270
149
MMP9_HUMAN
124-174
51
1
A:124-174
51
1.4
ENST00000372330
4
ENSE00000845117
chr20:
44639561-44639689
129
MMP9_HUMAN
174-217
44
1
A:174-217
44
1.5
ENST00000372330
5
ENSE00000845118
chr20:
44639782-44639955
174
MMP9_HUMAN
217-275
59
1
A:217-275
59
1.6
ENST00000372330
6
ENSE00000845119
chr20:
44640213-44640386
174
MMP9_HUMAN
275-333
59
1
A:275-333
59
1.7
ENST00000372330
7
ENSE00000845120
chr20:
44640776-44640952
177
MMP9_HUMAN
333-392
60
1
A:333-392
60
1.8
ENST00000372330
8
ENSE00000845121
chr20:
44641066-44641221
156
MMP9_HUMAN
392-444
53
1
A:392-444
53
1.9
ENST00000372330
9
ENSE00000845122
chr20:
44641894-44642173
280
MMP9_HUMAN
444-537
94
1
A:444-444
1
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
(3, 5)
Info
All SCOP Domains
1a: SCOP_d1l6ja1 (A:29-105)
2a: SCOP_d1l6ja2 (A:106-215,A:391-444)
3a: SCOP_d1l6ja3 (A:216-274)
3b: SCOP_d1l6ja4 (A:275-331)
3c: SCOP_d1l6ja5 (A:332-390)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
PGBD-like
(9)
Superfamily
:
PGBD-like
(9)
Family
:
MMP N-terminal domain
(6)
Protein domain
:
Gelatinase B (MMP-9)
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d1l6ja1
A:29-105
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)
2a
d1l6ja2
A:106-215,A:391-444
Class
:
Small proteins
(3458)
Fold
:
Kringle-like
(68)
Superfamily
:
Kringle-like
(68)
Family
:
Fibronectin type II module
(13)
Protein domain
:
Gelatinase B (MMP-9) type II modules
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
3a
d1l6ja3
A:216-274
3b
d1l6ja4
A:275-331
3c
d1l6ja5
A:332-390
[
close SCOP info
]
CATH Domains
(3, 5)
Info
all CATH domains
1a: CATH_1l6jA02 (A:105-215,A:390-444)
2a: CATH_1l6jA01 (A:40-104)
3a: CATH_1l6jA05 (A:334-389)
3b: CATH_1l6jA03 (A:217-273)
3c: CATH_1l6jA04 (A:274-333)
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Architectures
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)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
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
1l6jA02
A:105-215,A:390-444
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Muramoyl-pentapeptide Carboxypeptidase; domain 1
(3)
Homologous Superfamily
:
Muramoyl-pentapeptide Carboxypeptidase, domain 1
(3)
Human (Homo sapiens)
(2)
2a
1l6jA01
A:40-104
Class
:
Mainly Beta
(13760)
Architecture
:
Ribbon
(789)
Topology
:
Seminal Fluid Protein PDC-109 (Domain B)
(33)
Homologous Superfamily
:
[code=2.10.10.10, no name defined]
(13)
Human (Homo sapiens)
(11)
3a
1l6jA05
A:334-389
3b
1l6jA03
A:217-273
3c
1l6jA04
A:274-333
[
close CATH info
]
Pfam Domains
(3, 5)
Info
all PFAM domains
1a: PFAM_PG_binding_1_1l6jA01 (A:38-94)
2a: PFAM_Peptidase_M10_1l6jA02 (A:115-444)
3a: PFAM_fn2_1l6jA03 (A:347-388)
3b: PFAM_fn2_1l6jA04 (A:347-388)
3c: PFAM_fn2_1l6jA05 (A:347-388)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PGBD
(5)
Family
:
PG_binding_1
(4)
Homo sapiens (Human)
(3)
1a
PG_binding_1-1l6jA01
A:38-94
Clan
:
Peptidase_MA
(251)
Family
:
Peptidase_M10
(85)
Homo sapiens (Human)
(82)
2a
Peptidase_M10-1l6jA02
A:115-444
Clan
:
no clan defined [family: fn2]
(6)
Family
:
fn2
(6)
Homo sapiens (Human)
(6)
3a
fn2-1l6jA03
A:347-388
3b
fn2-1l6jA04
A:347-388
3c
fn2-1l6jA05
A:347-388
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Asymmetric Unit 1
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