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2OGA
Biol. Unit 1
Info
Asym.Unit (259 KB)
Biol.Unit 1 (131 KB)
Biol.Unit 2 (126 KB)
Biol.Unit 3 (252 KB)
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(1)
Title
:
X-RAY CRYSTAL STRUCTURE OF S. VENEZUELAE DESV IN COMPLEX WITH KETIMINE INTERMEDIATE
Authors
:
H. M. Holden, E. S. Burgie
Date
:
05 Jan 07 (Deposition) - 15 May 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.05
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: A,B,C,D (1x)
Keywords
:
Plp-Dependent Enzyme, Desosamine, Transaminase, Deoxysugars, Antibiotics, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. S. Burgie, J. B. Thoden, H. M. Holden
Molecular Architecture Of Desv From Streptomyces Venezuelae: A Plp-Dependent Transaminase Involved In The Biosynthesis Of The Unusual Sugar Desosamine.
Protein Sci. V. 16 887 2007
(for further references see the
PDB file header
)
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Hetero Components
(2, 6)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
4a: N-({3-HYDROXY-2-METHYL-5-[(PHOSPHO... (PGUa)
4b: N-({3-HYDROXY-2-METHYL-5-[(PHOSPHO... (PGUb)
4c: N-({3-HYDROXY-2-METHYL-5-[(PHOSPHO... (PGUc)
4d: N-({3-HYDROXY-2-METHYL-5-[(PHOSPHO... (PGUd)
View:
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Label:
No.
Name
Count
Type
Full Name
1
CL
-1
Ligand/Ion
CHLORIDE ION
2
EDO
4
Ligand/Ion
1,2-ETHANEDIOL
3
NA
-1
Ligand/Ion
SODIUM ION
4
PGU
2
Ligand/Ion
N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-GLUTAMIC ACID
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Sites
(10, 10)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC6 (SOFTWARE)
04: AC7 (SOFTWARE)
05: AC8 (SOFTWARE)
06: AC9 (SOFTWARE)
07: BC1 (SOFTWARE)
08: BC2 (SOFTWARE)
09: BC3 (SOFTWARE)
10: BC4 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:39 , LEU A:40
BINDING SITE FOR RESIDUE CL A 380
02
AC2
SOFTWARE
HOH A:1181 , TYR B:39 , LEU B:40
BINDING SITE FOR RESIDUE CL B 380
03
AC6
SOFTWARE
ASN A:65 , HOH A:1040 , HOH A:1041 , HOH A:1043 , ASN B:65 , HOH B:1024
BINDING SITE FOR RESIDUE NA A 1022
04
AC7
SOFTWARE
TYR A:55 , GLU A:57 , ARG A:172 , ARG A:177 , HOH A:1124 , ASP D:308
BINDING SITE FOR RESIDUE EDO A 1023
05
AC8
SOFTWARE
PRO B:191 , LYS B:193 , ASN B:194 , PRO B:355 , HOH B:1064 , HOH B:1065 , HOH B:1103
BINDING SITE FOR RESIDUE EDO B 381
06
AC9
SOFTWARE
ARG A:224 , HIS C:60
BINDING SITE FOR RESIDUE EDO C 1026
07
BC1
SOFTWARE
PRO A:191 , LYS A:193 , ASN A:194 , PRO A:355 , HOH A:1068 , HOH A:1106 , HOH A:1287
BINDING SITE FOR RESIDUE EDO A 1024
08
BC2
SOFTWARE
ARG B:172 , ARG B:177 , ASP B:254 , HOH B:1061 , HOH B:1259
BINDING SITE FOR RESIDUE EDO B 382
09
BC3
SOFTWARE
SER A:66 , GLY A:67 , TYR A:93 , ALA A:95 , ASP A:164 , ALA A:166 , GLN A:167 , SER A:188 , TYR A:190 , LYS A:193 , TYR A:318 , HOH A:1069 , HOH A:1290 , TYR B:221 , TYR B:227 , ASN B:235 , ARG B:237
BINDING SITE FOR RESIDUE PGU A 1020
10
BC4
SOFTWARE
TYR A:221 , LYS A:226 , TYR A:227 , ASN A:235 , ARG A:237 , SER B:66 , GLY B:67 , TYR B:93 , ALA B:95 , ASP B:164 , ALA B:166 , GLN B:167 , SER B:188 , TYR B:190 , LYS B:193 , TYR B:318 , HOH B:1066 , HOH B:1200
BINDING SITE FOR RESIDUE PGU B 1021
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(, 0)
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Exons
(0, 0)
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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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2ogaa_ (A:)
1b: SCOP_d2ogab_ (B:)
1c: SCOP_d2ogac_ (C:)
1d: SCOP_d2ogad_ (D:)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PLP-dependent transferase-like
(627)
Superfamily
:
PLP-dependent transferases
(625)
Family
:
automated matches
(163)
Protein domain
:
automated matches
(163)
Streptomyces venezuelae [TaxId: 54571]
(2)
1a
d2ogaa_
A:
1b
d2ogab_
B:
1c
d2ogac_
C:
1d
d2ogad_
D:
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2ogaA01 (A:7-110,A:117-252)
1b: CATH_2ogaB01 (B:7-110,B:117-252)
1c: CATH_2ogaD01 (D:7-110,D:117-252)
1d: CATH_2ogaC01 (C:8-110,C:117-252)
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Organisms
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)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Aspartate Aminotransferase; domain 2
(384)
Homologous Superfamily
:
Type I PLP-dependent aspartate aminotransferase-like (Major domain)
(384)
Streptomyces venezuelae. Organism_taxid: 54571.
(2)
1a
2ogaA01
A:7-110,A:117-252
1b
2ogaB01
B:7-110,B:117-252
1c
2ogaD01
D:7-110,D:117-252
1d
2ogaC01
C:8-110,C:117-252
[
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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Show PDB file:
Asym.Unit (259 KB)
Header - Asym.Unit
Biol.Unit 1 (131 KB)
Header - Biol.Unit 1
Biol.Unit 2 (126 KB)
Header - Biol.Unit 2
Biol.Unit 3 (252 KB)
Header - Biol.Unit 3
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