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1CA1
Asym. Unit
Info
Asym.Unit (73 KB)
Biol.Unit 1 (66 KB)
Biol.Unit 2 (130 KB)
Biol.Unit 3 (130 KB)
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(1)
Title
:
ALPHA-TOXIN FROM CLOSTRIDIUM PERFRINGENS
Authors
:
C. E. Naylor, A. K. Basak, R. W. Titball
Date
:
22 Apr 98 (Deposition) - 04 May 99 (Release) - 16 Nov 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Biol. Unit 2: A (2x)
Biol. Unit 3: A (2x)
Keywords
:
Zinc Phospholipase C, Gangrene Determinant, C2 Domain, Ca And Membrane Binding, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. E. Naylor, J. T. Eaton, A. Howells, N. Justin, D. S. Moss, R. W. Titball, A. K. Basak
Structure Of The Key Toxin In Gas Gangrene.
Nat. Struct. Biol. V. 5 738 1998
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 13)
Info
All Hetero Components
1a: CADMIUM ION (CDa)
1b: CADMIUM ION (CDb)
1c: CADMIUM ION (CDc)
1d: CADMIUM ION (CDd)
1e: CADMIUM ION (CDe)
1f: CADMIUM ION (CDf)
1g: CADMIUM ION (CDg)
1h: CADMIUM ION (CDh)
1i: CADMIUM ION (CDi)
1j: CADMIUM ION (CDj)
1k: CADMIUM ION (CDk)
1l: CADMIUM ION (CDl)
2a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CD
12
Ligand/Ion
CADMIUM ION
2
ZN
1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(26, 26)
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: C10 (UNKNOWN)
15: C11 (UNKNOWN)
16: C12 (UNKNOWN)
17: CA1 (UNKNOWN)
18: CD2 (UNKNOWN)
19: CD3 (UNKNOWN)
20: CD4 (UNKNOWN)
21: CD5 (UNKNOWN)
22: CD6 (UNKNOWN)
23: CD7 (UNKNOWN)
24: CD8 (UNKNOWN)
25: CD9 (UNKNOWN)
26: ZN1 (UNKNOWN)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TRP A:1 , HIS A:11 , ASP A:130 , CD A:373 , HOH A:573
BINDING SITE FOR RESIDUE ZN A 371
02
AC2
SOFTWARE
HIS A:136 , HIS A:148 , GLU A:152 , HOH A:483 , HOH A:573
BINDING SITE FOR RESIDUE CD A 372
03
AC3
SOFTWARE
ASP A:56 , HIS A:68 , HIS A:126 , ASP A:130 , ZN A:371 , HOH A:572
BINDING SITE FOR RESIDUE CD A 373
04
AC4
SOFTWARE
GLY A:168 , CYS A:169 , HIS A:207 , HOH A:476 , HOH A:477 , HOH A:492
BINDING SITE FOR RESIDUE CD A 374
05
AC5
SOFTWARE
CYS A:169 , GLU A:173 , ASP A:216 , HOH A:480 , HOH A:482
BINDING SITE FOR RESIDUE CD A 375
06
AC6
SOFTWARE
GLU A:173 , HIS A:212 , ASP A:216 , HOH A:494 , HOH A:496
BINDING SITE FOR RESIDUE CD A 376
07
AC7
SOFTWARE
ASP A:174 , ASP A:178 , HOH A:403 , HOH A:409 , HOH A:455 , HOH A:527
BINDING SITE FOR RESIDUE CD A 377
08
AC8
SOFTWARE
HIS A:241 , GLU A:245 , HOH A:475
BINDING SITE FOR RESIDUE CD A 378
09
AC9
SOFTWARE
ASP A:63 , ASP A:293 , HOH A:555
BINDING SITE FOR RESIDUE CD A 379
10
BC1
SOFTWARE
HIS A:46 , GLU A:359 , HOH A:525 , HOH A:545
BINDING SITE FOR RESIDUE CD A 380
11
BC2
SOFTWARE
GLU A:157 , HOH A:407 , HOH A:516
BINDING SITE FOR RESIDUE CD A 381
12
BC3
SOFTWARE
ASP A:273 , ASN A:297 , HOH A:422 , HOH A:427
BINDING SITE FOR RESIDUE CD A 382
13
BC4
SOFTWARE
ASP A:269 , GLY A:271 , ASP A:336 , ALA A:337 , HOH A:495 , HOH A:561
BINDING SITE FOR RESIDUE CD A 383
14
C10
UNKNOWN
HIS A:46 , GLU A:359
CD FROM CRYSTALLISATION BUFFER AT PROTEIN SURFACE.
15
C11
UNKNOWN
GLU A:157
CD FROM CRYSTALLISATION BUFFER AT PROTEIN SURFACE.
16
C12
UNKNOWN
ASP A:273 , ASN A:297
CD FROM CRYSTALLISATION BUFFER AT PROTEIN SURFACE. POSSIBLE CA BINDING SITE.
17
CA1
UNKNOWN
ASP A:336 , ALA A:337 , ASP A:269 , GLY A:271
POSSIBLE CA BINDING SITE. CURRENTLY LOW OCCUPANCY CD ION (RESIDUE 383)
18
CD2
UNKNOWN
HIS A:136 , HIS A:148 , GLU A:152
2ND ZINC BINDING SITE, CONTAINING CD FROM CRYSTALLISATION BUFFER.
19
CD3
UNKNOWN
ASP A:130 , HIS A:68 , HIS A:126 , ASP A:56
3ND ZINC BINDING SITE, CONTAINING CD FROM CRYSTALLISATION BUFFER.
20
CD4
UNKNOWN
GLY A:168 , CYS A:169 , HIS A:207
CD FROM CRYSTALLISATION BUFFER AT PROTEIN SURFACE.
21
CD5
UNKNOWN
CYS A:169 , GLU A:173 , ASP A:216
CD FROM CRYSTALLISATION BUFFER AT PROTEIN SURFACE.
22
CD6
UNKNOWN
GLU A:173 , HIS A:212 , ASP A:216
CD FROM CRYSTALLISATION BUFFER AT PROTEIN SURFACE.
23
CD7
UNKNOWN
ASP A:174 , ASP A:178
CD FROM CRYSTALLISATION BUFFER AT PROTEIN SURFACE.
24
CD8
UNKNOWN
HIS A:241 , GLU A:245
CD FROM CRYSTALLISATION BUFFER AT PROTEIN SURFACE.
25
CD9
UNKNOWN
ASP A:293 , ASP A:63
CD FROM CRYSTALLISATION BUFFER AT PROTEIN SURFACE.
26
ZN1
UNKNOWN
TRP A:1 , HIS A:11 , ASP A:130
ZINC BINDING SITE AT ACTIVE SITE.
[
close Site info
]
SAPs(SNPs)/Variants
(15, 15)
Info
(mutated residues are not available)
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 (V167V, chain A, )
09: VAR_PHLC1_CLOPE_015 (D174A, chain A, )
10: VAR_PHLC1_CLOPE_016 (A177T, chain A, )
11: VAR_PHLC1_CLOPE_017 (K253N, chain A, )
12: VAR_PHLC1_CLOPE_018 (T301A, chain A, )
13: VAR_PHLC1_CLOPE_019 (P335S, chain A, )
14: VAR_PHLC1_CLOPE_020 (V345L, chain A, )
15: VAR_PHLC1_CLOPE_021 (V345V, 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
V
167
V
09
UniProt
VAR_PHLC1_CLOPE_015
*
D
202
A
PHLC1_CLOPE
---
---
A
D
174
A
10
UniProt
VAR_PHLC1_CLOPE_016
*
A
205
T
PHLC1_CLOPE
---
---
A
A
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
P
335
S
14
UniProt
VAR_PHLC1_CLOPE_020
*
I
373
L
PHLC1_CLOPE
---
---
A
V
345
L
15
UniProt
VAR_PHLC1_CLOPE_021
*
I
373
V
PHLC1_CLOPE
---
---
A
V
345
V
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: PROKAR_ZN_DEPEND_PLPC_1 (A:126-139,A:126-139)
2: PLAT (A:256-370,A:256-370)
;
View:
Select:
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
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d1ca1a1 (A:1-249)
2a: SCOP_d1ca1a2 (A:250-370)
View:
Select:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
d1ca1a1
A: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
d1ca1a2
A:250-370
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_1ca1A01 (A:1-250)
2a: CATH_1ca1A02 (A:251-370)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
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: cer89l43.
(1)
1a
1ca1A01
A:1-250
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Lipoxygenase-1
(46)
Homologous Superfamily
:
Lipoxygenase-1
(44)
Clostridium perfringens. Organism_taxid: 1502. Strain: cer89l43.
(1)
2a
1ca1A02
A:251-370
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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]
Atom Selection
(currently selected atoms:
all
)
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
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