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Getting 'Biological Unit' information from database.
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Getting 'Hetero Component' information from database.
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Getting 'Exon' information from database.
1EAK
Asym. Unit
Info
Asym.Unit (283 KB)
Biol.Unit 1 (140 KB)
Biol.Unit 2 (140 KB)
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(1)
Title
:
CATALYTIC DOMAIN OF PROMMP-2 E404Q MUTANT
Authors
:
U. Bergmann, A. Tuuttila, K. Tryggvason, E. Morgunova
Date
:
12 Jul 01 (Deposition) - 22 Aug 02 (Release) - 21 Dec 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.66
Chains
:
Asym. Unit : A,B,C,D,P,R
Biol. Unit 1: A,C,P (1x)
Biol. Unit 2: B,D,R (1x)
Keywords
:
Hydrolase-Hydrolase Inhibitor Complex, Hydrolyse, Matrix Metalloproteinase, Gelatinase A, Hydrolase- Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
U. Bergmann, A. Tuuttila, E. Morgunova, K. Tryggvason
Crystal Structure Of Human Mmp-2 Reveals A New P
To Be Published
[
close entry info
]
Hetero Components
(3, 22)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
1g: CALCIUM ION (CAg)
1h: CALCIUM ION (CAh)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
8
Ligand/Ion
CALCIUM ION
2
SO4
6
Ligand/Ion
SULFATE ION
3
ZN
8
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(24, 24)
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)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN A:298 , GLY A:299 , THR A:300 , THR C:307
BINDING SITE FOR RESIDUE SO4 A 851
02
AC2
SOFTWARE
HIS A:178 , ASP A:180 , HIS A:193 , HIS A:206
BINDING SITE FOR RESIDUE ZN A 996
03
AC3
SOFTWARE
CYS A:102 , HIS A:403 , HIS A:407 , HIS A:413
BINDING SITE FOR RESIDUE ZN A 997
04
AC4
SOFTWARE
ASP A:185 , GLY A:186 , ASP A:188 , LEU A:190 , ASP A:208 , GLU A:211
BINDING SITE FOR RESIDUE CA A 998
05
AC5
SOFTWARE
ALA A:167 , ASP A:168 , GLY A:198 , GLY A:200 , GLY A:202
BINDING SITE FOR RESIDUE CA A 999
06
AC6
SOFTWARE
GLN B:298 , GLY B:299 , THR B:300 , THR D:307 , ALA R:753
BINDING SITE FOR RESIDUE SO4 B 852
07
AC7
SOFTWARE
LYS B:242 , TYR B:244 , ASN B:245 , SER B:246
BINDING SITE FOR RESIDUE SO4 B 853
08
AC8
SOFTWARE
HIS B:178 , ASP B:180 , HIS B:193 , HIS B:206
BINDING SITE FOR RESIDUE ZN B 996
09
AC9
SOFTWARE
CYS B:102 , HIS B:403 , HIS B:407 , HIS B:413
BINDING SITE FOR RESIDUE ZN B 997
10
BC1
SOFTWARE
ASP B:185 , GLY B:186 , ASP B:188 , LEU B:190 , ASP B:208 , GLU B:211
BINDING SITE FOR RESIDUE CA B 998
11
BC2
SOFTWARE
ASP B:168 , GLY B:198 , GLY B:200 , GLY B:202
BINDING SITE FOR RESIDUE CA B 999
12
BC3
SOFTWARE
THR A:307 , GLN C:298 , GLY C:299 , THR C:300 , ALA P:753
BINDING SITE FOR RESIDUE SO4 C 850
13
BC4
SOFTWARE
ARG C:432 , SER C:434 , GLN C:435
BINDING SITE FOR RESIDUE SO4 C 856
14
BC5
SOFTWARE
HIS C:178 , ASP C:180 , HIS C:193 , HIS C:206
BINDING SITE FOR RESIDUE ZN C 996
15
BC6
SOFTWARE
CYS C:102 , HIS C:403 , HIS C:407 , HIS C:413
BINDING SITE FOR RESIDUE ZN C 997
16
BC7
SOFTWARE
ASP C:185 , GLY C:186 , ASP C:188 , LEU C:190 , ASP C:208 , GLU C:211
BINDING SITE FOR RESIDUE CA C 998
17
BC8
SOFTWARE
ASP C:168 , GLY C:198 , GLY C:200 , GLY C:202
BINDING SITE FOR RESIDUE CA C 999
18
BC9
SOFTWARE
THR B:307 , GLY D:299 , THR D:300
BINDING SITE FOR RESIDUE SO4 D 857
19
CC1
SOFTWARE
HIS D:178 , ASP D:180 , HIS D:193 , HIS D:206
BINDING SITE FOR RESIDUE ZN D 996
20
CC2
SOFTWARE
CYS D:102 , HIS D:403 , HIS D:407 , HIS D:413
BINDING SITE FOR RESIDUE ZN D 997
21
CC3
SOFTWARE
ASP D:185 , GLY D:186 , ASP D:188 , LEU D:190 , ASP D:208 , GLU D:211
BINDING SITE FOR RESIDUE CA D 998
22
CC4
SOFTWARE
ALA D:167 , ASP D:168 , GLY D:200 , GLY D:202
BINDING SITE FOR RESIDUE CA D 999
23
CC5
SOFTWARE
GLY A:130 , TYR A:131 , PRO A:133 , ASP A:209 , HIS A:276 , GLU A:277 , ALA A:278 , PHE A:293 , ASP A:303 , SER A:304 , ARG C:296 , GLY C:299 , SER C:301 , SO4 C:850
BINDING SITE FOR CHAIN P OF INHIBITOR PEPTIDE
24
CC6
SOFTWARE
ARG B:296 , GLN B:298 , GLY B:299 , THR B:300 , SER B:301 , SO4 B:852 , PRO D:133 , ASP D:209 , HIS D:276 , GLU D:277 , ALA D:278 , PHE D:293 , SER D:304 , THR D:306
BINDING SITE FOR CHAIN R OF INHIBITOR PEPTIDE
[
close Site info
]
SAPs(SNPs)/Variants
(6, 24)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_032423 (R101H, chain A/B/C/D, )
2: VAR_032424 (D210Y, chain A/B/C/D, )
3: VAR_036136 (A228T, chain A/B/C/D, )
4: VAR_MMP2_HUMAN_CCDS10752_1_01 (A228T, chain A/B/C/D, )
5: VAR_032425 (Q404K, chain A/B/C/D, )
6: VAR_020616 (A447V, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_032423
R
101
H
MMP2_HUMAN
Disease (MONA)
---
A/B/C/D
R
101
H
2
UniProt
VAR_032424
D
210
Y
MMP2_HUMAN
Polymorphism
---
A/B/C/D
D
210
Y
3
UniProt
VAR_036136
A
228
T
MMP2_HUMAN
Unclassified
---
A/B/C/D
A
228
T
4
CancerSNP
VAR_MMP2_HUMAN_CCDS10752_1_01
*
A
228
T
MMP2_HUMAN
Disease (Colorectal cancer)
---
A/B/C/D
A
228
T
5
UniProt
VAR_032425
E
404
K
MMP2_HUMAN
Disease (MONA)
---
A/B/C/D
Q
404
K
6
UniProt
VAR_020616
A
447
V
MMP2_HUMAN
Polymorphism
17859943
A/B/C/D
A
447
V
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(4, 32)
Info
All PROSITE Patterns/Profiles
1: CYSTEINE_SWITCH (A:100-107,B:100-107,C:100-107,D:10...)
2: FN2_2 (A:228-276,B:228-276,C:228-276,D:22...)
3: FN2_1 (A:233-274,B:233-274,C:233-274,D:23...)
4: ZINC_PROTEASE (A:400-409,B:400-409,C:400-409,D:40...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CYSTEINE_SWITCH
PS00546
Matrixins cysteine switch.
MMP2_HUMAN
100-107
4
A:100-107
B:100-107
C:100-107
D:100-107
2
FN2_2
PS51092
Fibronectin type-II collagen-binding domain profile.
MMP2_HUMAN
228-276
286-334
344-392
12
A:228-276
B:228-276
C:228-276
D:228-276
A:286-334
B:286-334
C:286-334
D:286-334
A:344-392
B:344-392
C:344-392
D:344-392
3
FN2_1
PS00023
Fibronectin type-II collagen-binding domain signature.
MMP2_HUMAN
233-274
291-332
349-390
12
A:233-274
B:233-274
C:233-274
D:233-274
A:291-332
B:291-332
C:291-332
D:291-332
A:349-390
B:349-390
C:349-390
D:349-390
4
ZINC_PROTEASE
PS00142
Neutral zinc metallopeptidases, zinc-binding region signature.
MMP2_HUMAN
400-409
4
A:400-409
B:400-409
C:400-409
D:400-409
[
close PROSITE info
]
Exons
(9, 36)
Info
All Exons
Exon 1.1 (A:32-51 | B:32-51 | C:32-51 | D:32...)
Exon 1.3 (A:52-127 | B:52-127 | C:52-127 | D...)
Exon 1.4 (A:127-177 | B:127-177 | C:127-177 ...)
Exon 1.5 (A:177-220 | B:177-220 | C:177-220 ...)
Exon 1.6 (A:220-278 | B:220-278 | C:220-278 ...)
Exon 1.7 (A:278-336 | B:278-336 | C:278-336 ...)
Exon 1.8 (A:336-394 | B:336-394 | C:336-394 ...)
Exon 1.9 (A:394-446 | B:394-446 | C:394-446 ...)
Exon 1.10 (A:446-452 | B:446-450 | C:446-449 ...)
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
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
4
A:32-51
B:32-51
C:32-51
D:32-51
20
20
20
20
1.3
ENST00000219070
3
ENSE00000684353
chr16:
55516821-55517047
227
MMP2_HUMAN
52-127
76
4
A:52-127
B:52-127
C:52-127
D:52-127
76
76
76
76
1.4
ENST00000219070
4
ENSE00000684376
chr16:
55517928-55518076
149
MMP2_HUMAN
127-177
51
4
A:127-177
B:127-177
C:127-177
D:127-177
51
51
51
51
1.5
ENST00000219070
5
ENSE00000684379
chr16:
55519211-55519339
129
MMP2_HUMAN
177-220
44
4
A:177-220
B:177-220
C:177-220
D:177-220
44
44
44
44
1.6
ENST00000219070
6
ENSE00000684383
chr16:
55519516-55519689
174
MMP2_HUMAN
220-278
59
4
A:220-278
B:220-278
C:220-278
D:220-278
59
59
59
59
1.7
ENST00000219070
7
ENSE00000396666
chr16:
55522455-55522628
174
MMP2_HUMAN
278-336
59
4
A:278-336
B:278-336
C:278-336
D:278-336
59
59
59
59
1.8
ENST00000219070
8
ENSE00000684389
chr16:
55523563-55523736
174
MMP2_HUMAN
336-394
59
4
A:336-394
B:336-394
C:336-394
D:336-394
59
59
59
59
1.9
ENST00000219070
9
ENSE00001170187
chr16:
55525713-55525868
156
MMP2_HUMAN
394-446
53
4
A:394-446
B:394-446
C:394-446
D:394-446
53
53
53
53
1.10
ENST00000219070
10
ENSE00000684415
chr16:
55527070-55527205
136
MMP2_HUMAN
446-491
46
4
A:446-452
B:446-450
C:446-449
D:446-450
7
5
4
5
1.11
ENST00000219070
11
ENSE00000684425
chr16:
55530838-55530974
137
MMP2_HUMAN
491-537
47
0
-
-
1.12
ENST00000219070
12
ENSE00000684426
chr16:
55532201-55532360
160
MMP2_HUMAN
537-590
54
0
-
-
1.13
ENST00000219070
13
ENSE00000684427
chr16:
55536691-55536800
110
MMP2_HUMAN
590-627
38
0
-
-
1.14b
ENST00000219070
14b
ENSE00001931477
chr16:
55539251-55540603
1353
MMP2_HUMAN
627-660
34
0
-
-
[
close EXON info
]
SCOP Domains
(3, 20)
Info
All SCOP Domains
1a: SCOP_d1eaka1 (A:32-107)
1b: SCOP_d1eakb1 (B:32-107)
1c: SCOP_d1eakc1 (C:32-107)
1d: SCOP_d1eakd1 (D:32-107)
2a: SCOP_d1eaka2 (A:108-216,A:394-452)
2b: SCOP_d1eakb2 (B:108-216,B:394-450)
2c: SCOP_d1eakc2 (C:108-216,C:394-449)
2d: SCOP_d1eakd2 (D:108-216,D:394-450)
3a: SCOP_d1eaka3 (A:217-277)
3b: SCOP_d1eaka4 (A:278-335)
3c: SCOP_d1eakd4 (D:278-335)
3d: SCOP_d1eakd5 (D:336-393)
3e: SCOP_d1eaka5 (A:336-393)
3f: SCOP_d1eakb3 (B:217-277)
3g: SCOP_d1eakb4 (B:278-335)
3h: SCOP_d1eakb5 (B:336-393)
3i: SCOP_d1eakc3 (C:217-277)
3j: SCOP_d1eakc4 (C:278-335)
3k: SCOP_d1eakc5 (C:336-393)
3l: SCOP_d1eakd3 (D:217-277)
View:
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Classes
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)
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)
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
d1eaka1
A:32-107
1b
d1eakb1
B:32-107
1c
d1eakc1
C:32-107
1d
d1eakd1
D:32-107
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)
2a
d1eaka2
A:108-216,A:394-452
2b
d1eakb2
B:108-216,B:394-450
2c
d1eakc2
C:108-216,C:394-449
2d
d1eakd2
D:108-216,D:394-450
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)
3a
d1eaka3
A:217-277
3b
d1eaka4
A:278-335
3c
d1eakd4
D:278-335
3d
d1eakd5
D:336-393
3e
d1eaka5
A:336-393
3f
d1eakb3
B:217-277
3g
d1eakb4
B:278-335
3h
d1eakb5
B:336-393
3i
d1eakc3
C:217-277
3j
d1eakc4
C:278-335
3k
d1eakc5
C:336-393
3l
d1eakd3
D:217-277
[
close SCOP info
]
CATH Domains
(3, 20)
Info
all CATH domains
1a: CATH_1eakA02 (A:108-218,A:392-452)
1b: CATH_1eakB02 (B:108-218,B:392-450)
1c: CATH_1eakD02 (D:108-218,D:392-450)
1d: CATH_1eakC02 (C:108-218,C:392-449)
2a: CATH_1eakA01 (A:45-107)
2b: CATH_1eakB01 (B:45-107)
2c: CATH_1eakC01 (C:45-107)
2d: CATH_1eakD01 (D:45-107)
3a: CATH_1eakA05 (A:336-391)
3b: CATH_1eakA03 (A:220-276)
3c: CATH_1eakB03 (B:220-276)
3d: CATH_1eakC03 (C:220-276)
3e: CATH_1eakB05 (B:336-391)
3f: CATH_1eakD03 (D:220-276)
3g: CATH_1eakA04 (A:277-335)
3h: CATH_1eakB04 (B:277-335)
3i: CATH_1eakC04 (C:277-335)
3j: CATH_1eakD04 (D:277-335)
3k: CATH_1eakC05 (C:336-391)
3l: CATH_1eakD05 (D:336-391)
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
1eakA02
A:108-218,A:392-452
1b
1eakB02
B:108-218,B:392-450
1c
1eakD02
D:108-218,D:392-450
1d
1eakC02
C:108-218,C:392-449
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
1eakA01
A:45-107
2b
1eakB01
B:45-107
2c
1eakC01
C:45-107
2d
1eakD01
D:45-107
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
1eakA05
A:336-391
3b
1eakA03
A:220-276
3c
1eakB03
B:220-276
3d
1eakC03
C:220-276
3e
1eakB05
B:336-391
3f
1eakD03
D:220-276
3g
1eakA04
A:277-335
3h
1eakB04
B:277-335
3i
1eakC04
C:277-335
3j
1eakD04
D:277-335
3k
1eakC05
C:336-391
3l
1eakD05
D:336-391
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Asymmetric Unit 1
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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)
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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") .
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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") .
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