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1GXD
Asym. Unit
Info
Asym.Unit (265 KB)
Biol.Unit 1 (130 KB)
Biol.Unit 2 (131 KB)
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(1)
Title
:
PROMMP-2/TIMP-2 COMPLEX
Authors
:
E. Morgunova, A. Tuuttila, U. Bergmann, K. Tryggvason
Date
:
02 Apr 02 (Deposition) - 09 Jul 02 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B,D (1x)
Keywords
:
Hydrolase, Metalloprotease, Zymogen, Collagen Degradation, Extracellular Matrix, Gelatinase A, Matrix Metalloproteinase 2, Proteinase Inhibitor
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Morgunova, A. Tuuttila, U. Bergmann, K. Tryggvason
Structural Insight Into The Complex Formation Of Latent Matrix Metalloproteinase 2 With Tissue Inhibitor Of Metalloproteinase 2
Proc. Natl. Acad. Sci. Usa V. 99 7414 2002
[
close entry info
]
Hetero Components
(3, 8)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
SO4
2
Ligand/Ion
SULFATE ION
3
ZN
4
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(8, 8)
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: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLN A:269 , GLY A:270 , THR A:271 , THR B:278
BINDING SITE FOR RESIDUE SO4 A1632
2
AC2
SOFTWARE
HIS A:149 , ASP A:151 , HIS A:164 , HIS A:177
BINDING SITE FOR RESIDUE ZN A1633
3
AC3
SOFTWARE
CYS A:73 , ASN A:75 , HIS A:374 , HIS A:378 , HIS A:384
BINDING SITE FOR RESIDUE ZN A1634
4
AC4
SOFTWARE
ASP A:156 , GLY A:157 , ASP A:159 , LEU A:161 , ASP A:179 , GLU A:182
BINDING SITE FOR RESIDUE CA A1635
5
AC5
SOFTWARE
THR A:278 , GLN B:269 , GLY B:270 , THR B:271
BINDING SITE FOR RESIDUE SO4 B1632
6
AC6
SOFTWARE
HIS B:149 , ASP B:151 , HIS B:164 , HIS B:177
BINDING SITE FOR RESIDUE ZN B1633
7
AC7
SOFTWARE
CYS B:73 , ASN B:75 , HIS B:374 , HIS B:378 , HIS B:384
BINDING SITE FOR RESIDUE ZN B1634
8
AC8
SOFTWARE
ASP B:156 , GLY B:157 , ASP B:159 , LEU B:161 , ASP B:179 , GLU B:182
BINDING SITE FOR RESIDUE CA B1635
[
close Site info
]
SAPs(SNPs)/Variants
(11, 22)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_032423 (R72H, chain A/B, )
02: VAR_032424 (D181Y, chain A/B, )
03: VAR_036136 (A199T, chain A/B, )
04: VAR_MMP2_HUMAN_CCDS10752_1_01 (A199T, chain A/B, )
05: VAR_032425 (A375K, chain A/B, )
06: VAR_020616 (A418V, chain A/B, )
07: VAR_036137 (T469M, chain A/B, )
08: VAR_MMP2_HUMAN_CCDS10752_1_02 (T469M, chain A/B, )
09: VAR_020617 (V592L, chain A/B, )
10: VAR_036138 (S615I, chain A/B, )
11: VAR_MMP2_HUMAN_CCDS10752_1_03 (S615I, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_032423
R
101
H
MMP2_HUMAN
Disease (MONA)
---
A/B
R
72
H
02
UniProt
VAR_032424
D
210
Y
MMP2_HUMAN
Polymorphism
---
A/B
D
181
Y
03
UniProt
VAR_036136
A
228
T
MMP2_HUMAN
Unclassified
---
A/B
A
199
T
04
CancerSNP
VAR_MMP2_HUMAN_CCDS10752_1_01
*
A
228
T
MMP2_HUMAN
Disease (Colorectal cancer)
---
A/B
A
199
T
05
UniProt
VAR_032425
E
404
K
MMP2_HUMAN
Disease (MONA)
---
A/B
A
375
K
06
UniProt
VAR_020616
A
447
V
MMP2_HUMAN
Polymorphism
17859943
A/B
A
418
V
07
UniProt
VAR_036137
T
498
M
MMP2_HUMAN
Unclassified
---
A/B
T
469
M
08
CancerSNP
VAR_MMP2_HUMAN_CCDS10752_1_02
*
T
498
M
MMP2_HUMAN
Disease (Colorectal cancer)
---
A/B
T
469
M
09
UniProt
VAR_020617
V
621
L
MMP2_HUMAN
Polymorphism
16955280
A/B
V
592
L
10
UniProt
VAR_036138
S
644
I
MMP2_HUMAN
Unclassified
---
A/B
S
615
I
11
CancerSNP
VAR_MMP2_HUMAN_CCDS10752_1_03
*
S
644
I
MMP2_HUMAN
Disease (Colorectal cancer)
---
A/B
S
615
I
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(8, 30)
Info
All PROSITE Patterns/Profiles
1: NTR (C:1-126,D:1-126)
2: TIMP (C:1-13,D:1-13)
3: CYSTEINE_SWITCH (A:71-78,B:71-78)
4: FN2_2 (A:199-247,B:199-247|A:257-305,B:25...)
5: FN2_1 (A:204-245,B:204-245|A:262-303,B:26...)
6: ZINC_PROTEASE (A:371-380,B:371-380)
7: HEMOPEXIN_2 (A:443-487,B:443-487|A:488-534,B:48...)
8: HEMOPEXIN (A:577-592,B:577-592)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
NTR
PS50189
NTR domain profile.
TIMP2_HUMAN
27-152
2
C:1-126
D:1-126
2
TIMP
PS00288
Tissue inhibitors of metalloproteinases signature.
TIMP2_HUMAN
27-39
2
C:1-13
D:1-13
3
CYSTEINE_SWITCH
PS00546
Matrixins cysteine switch.
MMP2_HUMAN
100-107
2
A:71-78
B:71-78
4
FN2_2
PS51092
Fibronectin type-II collagen-binding domain profile.
MMP2_HUMAN
228-276
286-334
344-392
6
A:199-247
B:199-247
A:257-305
B:257-305
A:315-363
B:315-363
5
FN2_1
PS00023
Fibronectin type-II collagen-binding domain signature.
MMP2_HUMAN
233-274
291-332
349-390
6
A:204-245
B:204-245
A:262-303
B:262-303
A:320-361
B:320-361
6
ZINC_PROTEASE
PS00142
Neutral zinc metallopeptidases, zinc-binding region signature.
MMP2_HUMAN
400-409
2
A:371-380
B:371-380
7
HEMOPEXIN_2
PS51642
Hemopexin repeat profile.
MMP2_HUMAN
472-516
517-563
565-613
614-660
8
A:443-487
B:443-487
A:488-534
B:488-534
A:536-584
B:536-584
A:585-631
B:585-631
8
HEMOPEXIN
PS00024
Hemopexin domain signature.
MMP2_HUMAN
606-621
2
A:577-592
B:577-592
[
close PROSITE info
]
Exons
(18, 36)
Info
All Exons
Exon 1.1 (A:1-22 | B:2-22)
Exon 1.3 (A:23-98 | B:23-98)
Exon 1.4 (A:98-148 | B:98-148)
Exon 1.5 (A:148-191 | B:148-191)
Exon 1.6 (A:191-249 | B:191-249)
Exon 1.7 (A:249-307 | B:249-307)
Exon 1.8 (A:307-365 | B:307-365)
Exon 1.9 (A:365-417 | B:365-417)
Exon 1.10 (A:417-462 (gaps) | B:417-462 (gaps...)
Exon 1.11 (A:462-508 | B:462-508)
Exon 1.12 (A:508-561 | B:508-561)
Exon 1.13 (A:561-598 | B:561-598)
Exon 1.14b (A:598-631 | B:598-631)
Exon 2.1 (C:1-18 | D:1-18)
Exon 2.2b (C:18-51 | D:18-51)
Exon 2.3 (C:52-88 | D:52-88)
Exon 2.4a (C:88-129 | D:88-129)
Exon 2.5b (C:130-192 | D:130-192)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1
02: Boundary 1.1/1.3
03: Boundary 1.3/1.4
04: Boundary 1.4/1.5
05: Boundary 1.5/1.6
06: Boundary 1.6/1.7
07: Boundary 1.7/1.8
08: Boundary 1.8/1.9
09: Boundary 1.9/1.10
10: Boundary 1.10/1.11
11: Boundary 1.11/1.12
12: Boundary 1.12/1.13
13: Boundary 1.13/1.14b
14: Boundary 1.14b/-
15: Boundary -/2.1
16: Boundary 2.1/2.2b
17: Boundary 2.2b/2.3
18: Boundary 2.3/2.4a
19: Boundary 2.4a/2.5b
20: Boundary 2.5b/-
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
ENST00000219070
1
ENSE00001045278
chr16:
55512883-55513544
662
MMP2_HUMAN
1-51
51
2
A:1-22
B:2-22
22
21
1.3
ENST00000219070
3
ENSE00000684353
chr16:
55516821-55517047
227
MMP2_HUMAN
52-127
76
2
A:23-98
B:23-98
76
76
1.4
ENST00000219070
4
ENSE00000684376
chr16:
55517928-55518076
149
MMP2_HUMAN
127-177
51
2
A:98-148
B:98-148
51
51
1.5
ENST00000219070
5
ENSE00000684379
chr16:
55519211-55519339
129
MMP2_HUMAN
177-220
44
2
A:148-191
B:148-191
44
44
1.6
ENST00000219070
6
ENSE00000684383
chr16:
55519516-55519689
174
MMP2_HUMAN
220-278
59
2
A:191-249
B:191-249
59
59
1.7
ENST00000219070
7
ENSE00000396666
chr16:
55522455-55522628
174
MMP2_HUMAN
278-336
59
2
A:249-307
B:249-307
59
59
1.8
ENST00000219070
8
ENSE00000684389
chr16:
55523563-55523736
174
MMP2_HUMAN
336-394
59
2
A:307-365
B:307-365
59
59
1.9
ENST00000219070
9
ENSE00001170187
chr16:
55525713-55525868
156
MMP2_HUMAN
394-446
53
2
A:365-417
B:365-417
53
53
1.10
ENST00000219070
10
ENSE00000684415
chr16:
55527070-55527205
136
MMP2_HUMAN
446-491
46
2
A:417-462 (gaps)
B:417-462 (gaps)
46
46
1.11
ENST00000219070
11
ENSE00000684425
chr16:
55530838-55530974
137
MMP2_HUMAN
491-537
47
2
A:462-508
B:462-508
47
47
1.12
ENST00000219070
12
ENSE00000684426
chr16:
55532201-55532360
160
MMP2_HUMAN
537-590
54
2
A:508-561
B:508-561
54
54
1.13
ENST00000219070
13
ENSE00000684427
chr16:
55536691-55536800
110
MMP2_HUMAN
590-627
38
2
A:561-598
B:561-598
38
38
1.14b
ENST00000219070
14b
ENSE00001931477
chr16:
55539251-55540603
1353
MMP2_HUMAN
627-660
34
2
A:598-631
B:598-631
34
34
2.1
ENST00000262768
1
ENSE00001319888
chr17:
76921469-76921041
429
TIMP2_HUMAN
1-44
44
2
C:1-18
D:1-18
18
18
2.2b
ENST00000262768
2b
ENSE00001298704
chr17:
76870001-76869901
101
TIMP2_HUMAN
44-77
34
2
C:18-51
D:18-51
34
34
2.3
ENST00000262768
3
ENSE00000745851
chr17:
76867088-76866980
109
TIMP2_HUMAN
78-114
37
2
C:52-88
D:52-88
37
37
2.4a
ENST00000262768
4a
ENSE00001033832
chr17:
76853728-76853604
125
TIMP2_HUMAN
114-155
42
2
C:88-129
D:88-129
42
42
2.5b
ENST00000262768
5b
ENSE00001317697
chr17:
76851946-76849059
2888
TIMP2_HUMAN
156-220
65
2
C:130-192
D:130-192
63
63
[
close EXON info
]
SCOP Domains
(5, 14)
Info
All SCOP Domains
1a: SCOP_d1gxda1 (A:1-78)
1b: SCOP_d1gxdb1 (B:2-78)
2a: SCOP_d1gxda2 (A:429-631)
2b: SCOP_d1gxdb2 (B:429-631)
3a: SCOP_d1gxdc_ (C:)
3b: SCOP_d1gxdd_ (D:)
4a: SCOP_d1gxda3 (A:79-187,A:365-421)
4b: SCOP_d1gxdb3 (B:79-187,B:365-421)
5a: SCOP_d1gxda4 (A:188-248)
5b: SCOP_d1gxda5 (A:249-308)
5c: SCOP_d1gxda6 (A:309-364)
5d: SCOP_d1gxdb4 (B:188-248)
5e: SCOP_d1gxdb5 (B:249-308)
5f: SCOP_d1gxdb6 (B:309-364)
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 A (MMP-2)
(3)
Human (Homo sapiens) [TaxId: 9606]
(3)
1a
d1gxda1
A:1-78
1b
d1gxdb1
B:2-78
Class
:
All beta proteins
(24004)
Fold
:
4-bladed beta-propeller
(15)
Superfamily
:
Hemopexin-like domain
(15)
Family
:
Hemopexin-like domain
(12)
Protein domain
:
Gelatinase A (MMP-2), C-terminal domain
(4)
Human (Homo sapiens) [TaxId: 9606]
(4)
2a
d1gxda2
A:429-631
2b
d1gxdb2
B:429-631
Fold
:
OB-fold
(1179)
Superfamily
:
TIMP-like
(22)
Family
:
Tissue inhibitor of metalloproteinases, TIMP
(13)
Protein domain
:
TIMP-2
(7)
Human (Homo sapiens) [TaxId: 9606]
(4)
3a
d1gxdc_
C:
3b
d1gxdd_
D:
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 A
(4)
Human (Homo sapiens) [TaxId: 9606]
(4)
4a
d1gxda3
A:79-187,A:365-421
4b
d1gxdb3
B:79-187,B:365-421
Class
:
Small proteins
(3458)
Fold
:
Kringle-like
(68)
Superfamily
:
Kringle-like
(68)
Family
:
Fibronectin type II module
(13)
Protein domain
:
Gelatinase A (MMP-2) type II modules
(6)
Human (Homo sapiens) [TaxId: 9606]
(6)
5a
d1gxda4
A:188-248
5b
d1gxda5
A:249-308
5c
d1gxda6
A:309-364
5d
d1gxdb4
B:188-248
5e
d1gxdb5
B:249-308
5f
d1gxdb6
B:309-364
[
close SCOP info
]
CATH Domains
(5, 14)
Info
all CATH domains
1a: CATH_1gxdA01 (A:17-193,A:363-420)
1b: CATH_1gxdB01 (B:17-193,B:363-420)
2a: CATH_1gxdC01 (C:1-14,C:111-182)
2b: CATH_1gxdD01 (D:1-14,D:111-182)
3a: CATH_1gxdA05 (A:436-631)
3b: CATH_1gxdB05 (B:436-631)
4a: CATH_1gxdC02 (C:15-110)
4b: CATH_1gxdD02 (D:15-110)
5a: CATH_1gxdA04 (A:315-361)
5b: CATH_1gxdB03 (B:257-303)
5c: CATH_1gxdA02 (A:199-251)
5d: CATH_1gxdB02 (B:199-251)
5e: CATH_1gxdB04 (B:315-361)
5f: CATH_1gxdA03 (A:257-303)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
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
1gxdA01
A:17-193,A:363-420
1b
1gxdB01
B:17-193,B:363-420
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Tissue inhibitor of metalloproteinase-1. Chain B, domain 1
(6)
Homologous Superfamily
:
Tissue inhibitor of metalloproteinase-1. Chain B, domain 1
(6)
Human (Homo sapiens)
(6)
2a
1gxdC01
C:1-14,C:111-182
2b
1gxdD01
D:1-14,D:111-182
Class
:
Mainly Beta
(13760)
Architecture
:
4 Propellor
(14)
Topology
:
Hemopexin
(14)
Homologous Superfamily
:
Hemopexin
(14)
Human (Homo sapiens)
(10)
3a
1gxdA05
A:436-631
3b
1gxdB05
B:436-631
Architecture
:
Beta Barrel
(4804)
Topology
:
OB fold (Dihydrolipoamide Acetyltransferase, E2P)
(1040)
Homologous Superfamily
:
[code=2.40.50.120, no name defined]
(16)
Human (Homo sapiens)
(12)
4a
1gxdC02
C:15-110
4b
1gxdD02
D:15-110
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)
5a
1gxdA04
A:315-361
5b
1gxdB03
B:257-303
5c
1gxdA02
A:199-251
5d
1gxdB02
B:199-251
5e
1gxdB04
B:315-361
5f
1gxdA03
A:257-303
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
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RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
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pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
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Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
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Asym.Unit (265 KB)
Header - Asym.Unit
Biol.Unit 1 (130 KB)
Header - Biol.Unit 1
Biol.Unit 2 (131 KB)
Header - Biol.Unit 2
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