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2WY6
Biol. Unit 1
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
(1, 1)
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:
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Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
CD
-1
Ligand/Ion
CADMIUM ION
3
GOL
1
Ligand/Ion
GLYCEROL
4
ZN
-1
Ligand/Ion
ZINC ION
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Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC8 (SOFTWARE)
8: CC4 (SOFTWARE)
9: CC5 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TRP A:1 , HIS A:11 , ASP A:130 , CD A:1372
BINDING SITE FOR RESIDUE ZN A1371
2
AC2
SOFTWARE
ASP A:56 , HIS A:68 , HIS A:126 , ASP A:130 , ZN A:1371
BINDING SITE FOR RESIDUE CD A1372
3
AC3
SOFTWARE
HIS A:136 , HIS A:148 , GLU A:152
BINDING SITE FOR RESIDUE CD A1373
4
AC4
SOFTWARE
GLU A:157 , ASP A:215
BINDING SITE FOR RESIDUE CD A1374
5
AC5
SOFTWARE
GLU A:291 , HIS B:46 , GLU B:47
BINDING SITE FOR RESIDUE CD B1371
6
AC6
SOFTWARE
ASP A:293 , ASN A:294 , GLU B:43
BINDING SITE FOR RESIDUE CA A1375
7
AC8
SOFTWARE
HIS A:207 , ASP A:216 , TYR A:219
BINDING SITE FOR RESIDUE GOL A1376
8
CC4
SOFTWARE
HIS A:46 , GLU A:47 , GLU C:291 , ASP C:293
BINDING SITE FOR RESIDUE CD C1376
9
CC5
SOFTWARE
LYS A:115 , ASP C:293 , ASN C:294 , GLY C:296 , ASP C:298
BINDING SITE FOR RESIDUE CA C1377
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: PROKAR_ZN_DEPEND_PLPC_1 (A:126-139)
2: PLAT (A:256-370)
;
View:
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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
-
-
2
PLAT
PS50095
PLAT domain profile.
PHLC_CLOP1
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
(0, 0)
Info
All SCOP Domains
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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)
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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
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
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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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Organisms
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(
)
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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Chain A
Asymmetric Unit 1
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Show PDB file:
Asym.Unit (183 KB)
Header - Asym.Unit
Biol.Unit 1 (61 KB)
Header - Biol.Unit 1
Biol.Unit 2 (61 KB)
Header - Biol.Unit 2
Biol.Unit 3 (62 KB)
Header - Biol.Unit 3
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