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1QMD
Biol. Unit 1
Info
Asym.Unit (136 KB)
Biol.Unit 1 (67 KB)
Biol.Unit 2 (67 KB)
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(1)
Title
:
CALCIUM BOUND CLOSED FORM ALPHA-TOXIN FROM CLOSTRIDIUM PERFRINGENS
Authors
:
C. E. Naylor, J. Miller, R. W. Titball, A. K. Basak
Date
:
27 Sep 99 (Deposition) - 06 Feb 00 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Hydrolase, Zinc Phospholipase C, Gangrene Determinant, C2 Domain, Ca And Membrane Binding.
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. E. Naylor, M. Jepson, D. T. Crane, R. W. Titball, J. Miller, A. K. Basak, B. Bolgiano
Characterisation Of The Calcium-Binding C-Terminal Domain Of Clostridium Perfringens Alpha-Toxin
J. Mol. Biol. V. 294 757 1999
(for further references see the
PDB file header
)
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Hetero Components
(0, 0)
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)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
View:
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Label:
Sorry, no Info available
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TRP A:1 , HIS A:11 , ASP A:130 , ZN A:402 , HOH A:2023
BINDING SITE FOR RESIDUE ZN A 401
2
AC2
SOFTWARE
ASP A:56 , HIS A:68 , HIS A:126 , ASP A:130 , ZN A:401 , HOH A:2023
BINDING SITE FOR RESIDUE ZN A 402
3
AC3
SOFTWARE
ASP A:269 , GLY A:271 , ASP A:336 , ALA A:337 , GLU B:32
BINDING SITE FOR RESIDUE CA A 403
4
AC4
SOFTWARE
ASP A:293 , ASN A:294 , GLY A:296 , ASP A:298
BINDING SITE FOR RESIDUE CA A 404
5
AC5
SOFTWARE
THR A:272 , ASP A:273 , ASN A:297 , ASP A:298 , HOH A:2141
BINDING SITE FOR RESIDUE CA A 405
6
AC9
SOFTWARE
GLU A:32 , HOH A:2011 , ASP B:269 , GLY B:271 , ASP B:336 , ALA B:337
BINDING SITE FOR RESIDUE CA B 404
[
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]
SAPs(SNPs)/Variants
(15, 15)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_PHLC1_CLOPE_007 (V15A, chain A, )
02: VAR_PHLC1_CLOPE_008 (V19I, chain A, )
03: VAR_PHLC1_CLOPE_009 (L26M, chain A, )
04: VAR_PHLC1_CLOPE_010 (E43D, chain A, )
05: VAR_PHLC1_CLOPE_011 (D63N, chain A, )
06: VAR_PHLC1_CLOPE_012 (D75N, chain A, )
07: VAR_PHLC1_CLOPE_013 (H148Y, chain A, )
08: VAR_PHLC1_CLOPE_014 (A167V, chain A, )
09: VAR_PHLC1_CLOPE_015 (A174A, chain A, )
10: VAR_PHLC1_CLOPE_016 (T177T, chain A, )
11: VAR_PHLC1_CLOPE_017 (K253N, chain A, )
12: VAR_PHLC1_CLOPE_018 (T301A, chain A, )
13: VAR_PHLC1_CLOPE_019 (S335S, chain A, )
14: VAR_PHLC1_CLOPE_020 (I345L, chain A, )
15: VAR_PHLC1_CLOPE_021 (I345V, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_PHLC1_CLOPE_007
*
V
43
A
PHLC1_CLOPE
---
---
A
V
15
A
02
UniProt
VAR_PHLC1_CLOPE_008
*
V
47
I
PHLC1_CLOPE
---
---
A
V
19
I
03
UniProt
VAR_PHLC1_CLOPE_009
*
L
54
M
PHLC1_CLOPE
---
---
A
L
26
M
04
UniProt
VAR_PHLC1_CLOPE_010
*
E
71
D
PHLC1_CLOPE
---
---
A
E
43
D
05
UniProt
VAR_PHLC1_CLOPE_011
*
D
91
N
PHLC1_CLOPE
---
---
A
D
63
N
06
UniProt
VAR_PHLC1_CLOPE_012
*
D
103
N
PHLC1_CLOPE
---
---
A
D
75
N
07
UniProt
VAR_PHLC1_CLOPE_013
*
H
176
Y
PHLC1_CLOPE
---
---
A
H
148
Y
08
UniProt
VAR_PHLC1_CLOPE_014
*
A
195
V
PHLC1_CLOPE
---
---
A
A
167
V
09
UniProt
VAR_PHLC1_CLOPE_015
*
D
202
A
PHLC1_CLOPE
---
---
A
A
174
A
10
UniProt
VAR_PHLC1_CLOPE_016
*
A
205
T
PHLC1_CLOPE
---
---
A
T
177
T
11
UniProt
VAR_PHLC1_CLOPE_017
*
K
281
N
PHLC1_CLOPE
---
---
A
K
253
N
12
UniProt
VAR_PHLC1_CLOPE_018
*
T
329
A
PHLC1_CLOPE
---
---
A
T
301
A
13
UniProt
VAR_PHLC1_CLOPE_019
*
P
363
S
PHLC1_CLOPE
---
---
A
S
335
S
14
UniProt
VAR_PHLC1_CLOPE_020
*
I
373
L
PHLC1_CLOPE
---
---
A
I
345
L
15
UniProt
VAR_PHLC1_CLOPE_021
*
I
373
V
PHLC1_CLOPE
---
---
A
I
345
V
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: PROKAR_ZN_DEPEND_PLPC_1 (A:126-139)
2: PLAT (A:256-370)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PROKAR_ZN_DEPEND_PLPC_1
PS00384
Prokaryotic zinc-dependent phospholipase C signature.
PHLC_CLOP1
154-167
1
A:126-139
-
PHLC1_CLOPE
154-167
1
A:126-139
-
2
PLAT
PS50095
PLAT domain profile.
PHLC_CLOP1
284-398
1
A:256-370
-
PHLC1_CLOPE
284-398
1
A:256-370
-
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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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1qmda1 (A:1-249)
1b: SCOP_d1qmdb1 (B:1-249)
2a: SCOP_d1qmda2 (A:250-370)
2b: SCOP_d1qmdb2 (B:250-370)
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)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Phospholipase C/P1 nuclease
(20)
Superfamily
:
Phospholipase C/P1 nuclease
(20)
Family
:
Phospholipase C
(15)
Protein domain
:
Alpha-toxin, N-terminal domain
(7)
Clostridium perfringens, different strains [TaxId: 1502]
(6)
1a
d1qmda1
A:1-249
1b
d1qmdb1
B:1-249
Class
:
All beta proteins
(24004)
Fold
:
Lipase/lipooxygenase domain (PLAT/LH2 domain)
(47)
Superfamily
:
Lipase/lipooxygenase domain (PLAT/LH2 domain)
(47)
Family
:
Alpha-toxin, C-terminal domain
(7)
Protein domain
:
Alpha-toxin, C-terminal domain
(7)
Clostridium perfringens, different strains [TaxId: 1502]
(6)
2a
d1qmda2
A:250-370
2b
d1qmdb2
B:250-370
[
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1qmdA01 (A:1-250)
1b: CATH_1qmdB01 (B:1-250)
2a: CATH_1qmdA02 (A:251-370)
2b: CATH_1qmdB02 (B:251-370)
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)
(
)
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)
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
P1 Nuclease
(17)
Homologous Superfamily
:
P1 Nuclease
(17)
Clostridium perfringens. Organism_taxid: 1502. Strain: nctc8237.
(2)
1a
1qmdA01
A:1-250
1b
1qmdB01
B:1-250
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Lipoxygenase-1
(46)
Homologous Superfamily
:
Lipoxygenase-1
(44)
Clostridium perfringens. Organism_taxid: 1502. Strain: nctc8237.
(2)
2a
1qmdA02
A:251-370
2b
1qmdB02
B:251-370
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_PLAT_1qmdB01 (B:258-370)
1b: PFAM_PLAT_1qmdB02 (B:258-370)
2a: PFAM_Zn_dep_PLPC_1qmdB03 (B:10-227)
2b: PFAM_Zn_dep_PLPC_1qmdB04 (B:10-227)
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Clans
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Families
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(
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Organisms
(
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)
Clan
:
PLAT
(25)
Family
:
PLAT
(25)
Clostridium perfringens (strain ATCC 13124 / NCTC 8237 / Type A)
(4)
1a
PLAT-1qmdB01
B:258-370
1b
PLAT-1qmdB02
B:258-370
Clan
:
PhosC-NucP1
(7)
Family
:
Zn_dep_PLPC
(7)
Clostridium perfringens (strain ATCC 13124 / NCTC 8237 / Type A)
(4)
2a
Zn_dep_PLPC-1qmdB03
B:10-227
2b
Zn_dep_PLPC-1qmdB04
B:10-227
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