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2WY6
Asym. Unit
Info
Asym.Unit (183 KB)
Biol.Unit 1 (61 KB)
Biol.Unit 2 (61 KB)
Biol.Unit 3 (62 KB)
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(1)
Title
:
CLOSTRIDIUM PERFRINGENS ALPHA-TOXIN STRAIN NCTC8237 MUTANT T74I
Authors
:
S. G. Vachieri, C. E. Naylor, A. K. Basak
Date
:
12 Nov 09 (Deposition) - 24 Nov 09 (Release) - 11 May 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.20
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Keywords
:
Cytolysis, Hydrolase, Hemolysis, Membrane Binding, Virulence, Gangrene Determinant, C2 Domain
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. G. Vachieri, G. C. Clark, A. Alape-Giron, M. Flores-Diaz, N. Justin, C. E. Naylor, R. W. Titball, A. K. Basak
Comparison Of A Nontoxic Variant Of Clostridium Perfringens [Alpha]-Toxin With The Toxic Wild-Type Strain
Acta Crystallogr. , Sect. D V. 66 1067 2011
(for further references see the
PDB file header
)
[
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Hetero Components
(4, 24)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: CADMIUM ION (CDa)
2b: CADMIUM ION (CDb)
2c: CADMIUM ION (CDc)
2d: CADMIUM ION (CDd)
2e: CADMIUM ION (CDe)
2f: CADMIUM ION (CDf)
2g: CADMIUM ION (CDg)
2h: CADMIUM ION (CDh)
2i: CADMIUM ION (CDi)
2j: CADMIUM ION (CDj)
2k: CADMIUM ION (CDk)
2l: CADMIUM ION (CDl)
2m: CADMIUM ION (CDm)
2n: CADMIUM ION (CDn)
2o: CADMIUM ION (CDo)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
4c: ZINC ION (ZNc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
4
Ligand/Ion
CALCIUM ION
2
CD
15
Ligand/Ion
CADMIUM ION
3
GOL
2
Ligand/Ion
GLYCEROL
4
ZN
3
Ligand/Ion
ZINC ION
[
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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
TRP A:1 , HIS A:11 , ASP A:130 , CD A:1372
BINDING SITE FOR RESIDUE ZN A1371
02
AC2
SOFTWARE
ASP A:56 , HIS A:68 , HIS A:126 , ASP A:130 , ZN A:1371
BINDING SITE FOR RESIDUE CD A1372
03
AC3
SOFTWARE
HIS A:136 , HIS A:148 , GLU A:152
BINDING SITE FOR RESIDUE CD A1373
04
AC4
SOFTWARE
GLU A:157 , ASP A:215
BINDING SITE FOR RESIDUE CD A1374
05
AC5
SOFTWARE
GLU A:291 , HIS B:46 , GLU B:47
BINDING SITE FOR RESIDUE CD B1371
06
AC6
SOFTWARE
ASP A:293 , ASN A:294 , GLU B:43
BINDING SITE FOR RESIDUE CA A1375
07
AC7
SOFTWARE
GLU B:160 , HIS C:207 , TYR C:219
BINDING SITE FOR RESIDUE GOL C1371
08
AC8
SOFTWARE
HIS A:207 , ASP A:216 , TYR A:219
BINDING SITE FOR RESIDUE GOL A1376
09
AC9
SOFTWARE
TRP B:1 , HIS B:11 , HIS B:126 , ASP B:130 , CD B:1373
BINDING SITE FOR RESIDUE ZN B1372
10
BC1
SOFTWARE
ASP B:56 , HIS B:68 , HIS B:126 , ASP B:130 , ZN B:1372
BINDING SITE FOR RESIDUE CD B1373
11
BC2
SOFTWARE
HIS B:136 , HIS B:148 , GLU B:152
BINDING SITE FOR RESIDUE CD B1374
12
BC3
SOFTWARE
HIS B:212 , SER B:213 , ASP B:216
BINDING SITE FOR RESIDUE CD B1375
13
BC4
SOFTWARE
GLU B:291 , ASP B:293 , HIS C:46 , GLU C:47
BINDING SITE FOR RESIDUE CD B1376
14
BC5
SOFTWARE
ASP B:293 , ASN B:294 , GLY B:296 , ASP B:298 , LYS C:115
BINDING SITE FOR RESIDUE CA B1377
15
BC6
SOFTWARE
ASP B:269 , GLY B:271 , ASP B:336 , ALA B:337
BINDING SITE FOR RESIDUE CA B1378
16
BC7
SOFTWARE
ASP B:63 , GLU C:43
BINDING SITE FOR RESIDUE CD B1379
17
BC8
SOFTWARE
HIS B:241
BINDING SITE FOR RESIDUE CD B1380
18
BC9
SOFTWARE
TRP C:1 , HIS C:11 , ASP C:130 , CD C:1373
BINDING SITE FOR RESIDUE ZN C1372
19
CC1
SOFTWARE
ASP C:56 , HIS C:68 , HIS C:126 , ASP C:130 , ZN C:1372
BINDING SITE FOR RESIDUE CD C1373
20
CC2
SOFTWARE
HIS C:136 , HIS C:148 , GLU C:152
BINDING SITE FOR RESIDUE CD C1374
21
CC3
SOFTWARE
ASP C:216
BINDING SITE FOR RESIDUE CD C1375
22
CC4
SOFTWARE
HIS A:46 , GLU A:47 , GLU C:291 , ASP C:293
BINDING SITE FOR RESIDUE CD C1376
23
CC5
SOFTWARE
LYS A:115 , ASP C:293 , ASN C:294 , GLY C:296 , ASP C:298
BINDING SITE FOR RESIDUE CA C1377
24
CC6
SOFTWARE
HIS C:241
BINDING SITE FOR RESIDUE CD C1378
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 6)
Info
All PROSITE Patterns/Profiles
1: PROKAR_ZN_DEPEND_PLPC_1 (A:126-139,B:126-139,C:126-139)
2: PLAT (A:256-370,B:256-370,C: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
3
A:126-139
B:126-139
C:126-139
2
PLAT
PS50095
PLAT domain profile.
PHLC_CLOP1
284-398
3
A:256-370
B:256-370
C:256-370
[
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Exons
(0, 0)
Info
All Exons
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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
(0, 0)
Info
All SCOP Domains
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Sorry, no Info available
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CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_2wy6B01 (B:1-250)
1b: CATH_2wy6A01 (A:1-249)
1c: CATH_2wy6C01 (C:1-247)
2a: CATH_2wy6B02 (B:251-370)
2b: CATH_2wy6C02 (C:252-370)
2c: CATH_2wy6A02 (A:253-370)
View:
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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: nctc8237.
(2)
1a
2wy6B01
B:1-250
1b
2wy6A01
A:1-249
1c
2wy6C01
C:1-247
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
2wy6B02
B:251-370
2b
2wy6C02
C:252-370
2c
2wy6A02
A:253-370
[
close CATH info
]
Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_PLAT_2wy6C01 (C:258-370)
1b: PFAM_PLAT_2wy6C02 (C:258-370)
1c: PFAM_PLAT_2wy6C03 (C:258-370)
2a: PFAM_Zn_dep_PLPC_2wy6C04 (C:10-227)
2b: PFAM_Zn_dep_PLPC_2wy6C05 (C:10-227)
2c: PFAM_Zn_dep_PLPC_2wy6C06 (C:10-227)
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Clans
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)
(
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Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PLAT
(25)
Family
:
PLAT
(25)
Clostridium perfringens (strain ATCC 13124 / NCTC 8237 / Type A)
(4)
1a
PLAT-2wy6C01
C:258-370
1b
PLAT-2wy6C02
C:258-370
1c
PLAT-2wy6C03
C: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-2wy6C04
C:10-227
2b
Zn_dep_PLPC-2wy6C05
C:10-227
2c
Zn_dep_PLPC-2wy6C06
C:10-227
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Asymmetric Unit 1
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