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2OGE
Biol. Unit 2
Info
Asym.Unit (264 KB)
Biol.Unit 1 (131 KB)
Biol.Unit 2 (131 KB)
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(1)
Title
:
X-RAY STRUCTURE OF S. VENEZUELAE DESV IN ITS INTERNAL ALDIMINE FORM
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)
Keywords
:
Plp-Dependent Enzyme, Desosamine, Transaminase, Deoxysugars, Macrolide Antibiotics, Transferase
(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, 13)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
1e: CHLORIDE ION (CLe)
1f: CHLORIDE ION (CLf)
1g: CHLORIDE ION (CLg)
1h: CHLORIDE ION (CLh)
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)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
2n: 1,2-ETHANEDIOL (EDOn)
2o: 1,2-ETHANEDIOL (EDOo)
2p: 1,2-ETHANEDIOL (EDOp)
2q: 1,2-ETHANEDIOL (EDOq)
2r: 1,2-ETHANEDIOL (EDOr)
2s: 1,2-ETHANEDIOL (EDOs)
2t: 1,2-ETHANEDIOL (EDOt)
2u: 1,2-ETHANEDIOL (EDOu)
3a: 2-LYSINE(3-HYDROXY-2-METHYL-5-PHOS... (LLPa)
3b: 2-LYSINE(3-HYDROXY-2-METHYL-5-PHOS... (LLPb)
3c: 2-LYSINE(3-HYDROXY-2-METHYL-5-PHOS... (LLPc)
3d: 2-LYSINE(3-HYDROXY-2-METHYL-5-PHOS... (LLPd)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
-1
Ligand/Ion
CHLORIDE ION
2
EDO
11
Ligand/Ion
1,2-ETHANEDIOL
3
LLP
2
Mod. Amino Acid
2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
4
NA
-1
Ligand/Ion
SODIUM ION
[
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Sites
(16, 16)
Info
All Sites
01: AC6 (SOFTWARE)
02: AC7 (SOFTWARE)
03: AC8 (SOFTWARE)
04: AC9 (SOFTWARE)
05: BC1 (SOFTWARE)
06: CC1 (SOFTWARE)
07: CC2 (SOFTWARE)
08: CC3 (SOFTWARE)
09: CC4 (SOFTWARE)
10: CC5 (SOFTWARE)
11: CC6 (SOFTWARE)
12: CC9 (SOFTWARE)
13: DC1 (SOFTWARE)
14: DC2 (SOFTWARE)
15: DC3 (SOFTWARE)
16: DC4 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC6
SOFTWARE
TYR C:39 , LEU C:40 , HOH C:1343
BINDING SITE FOR RESIDUE CL C 1302
02
AC7
SOFTWARE
TYR C:227 , HIS C:229 , EDO C:1309 , HOH C:1533 , TYR D:318
BINDING SITE FOR RESIDUE CL C 1303
03
AC8
SOFTWARE
ASN C:65 , HOH C:1361 , HOH C:1528 , ASN D:65 , HOH D:1476 , HOH D:1477
BINDING SITE FOR RESIDUE NA C 1304
04
AC9
SOFTWARE
TYR D:39 , LEU D:40
BINDING SITE FOR RESIDUE CL D 1305
05
BC1
SOFTWARE
TYR C:318 , HIS D:229
BINDING SITE FOR RESIDUE CL D 1306
06
CC1
SOFTWARE
PHE C:12 , LEU C:13 , GLY C:192 , HIS C:291 , LEU C:292 , HOH C:1320 , HOH C:1322 , HOH C:1410
BINDING SITE FOR RESIDUE EDO C 1305
07
CC2
SOFTWARE
ARG C:151 , ARG C:176 , ARG C:177 , HOH C:1404 , HOH C:1521
BINDING SITE FOR RESIDUE EDO C 1306
08
CC3
SOFTWARE
PRO D:11 , PHE D:12 , LEU D:13 , ASP D:313 , HOH D:1486 , HOH D:1582
BINDING SITE FOR RESIDUE EDO D 1307
09
CC4
SOFTWARE
PRO D:191 , LLP D:193 , ASN D:194 , ARG D:249 , PRO D:355 , HOH D:1337 , HOH D:1419 , HOH D:1422
BINDING SITE FOR RESIDUE EDO D 1308
10
CC5
SOFTWARE
ASP C:27 , EDO C:1308 , ASP D:27
BINDING SITE FOR RESIDUE EDO C 1307
11
CC6
SOFTWARE
HIS D:113 , HIS D:116 , THR D:118 , ASP D:146 , HOH D:1392 , HOH D:1393 , HOH D:1403
BINDING SITE FOR RESIDUE EDO D 1309
12
CC9
SOFTWARE
GLY C:37 , LEU D:13 , ASP D:14 , LEU D:15 , LYS D:16 , HOH D:1318 , HOH D:1336 , HOH D:1486
BINDING SITE FOR RESIDUE EDO D 1310
13
DC1
SOFTWARE
ARG D:172 , ARG D:177 , HOH D:1534
BINDING SITE FOR RESIDUE EDO D 1311
14
DC2
SOFTWARE
ASP C:27 , ALA C:28 , EDO C:1307 , HOH C:1337
BINDING SITE FOR RESIDUE EDO C 1308
15
DC3
SOFTWARE
LYS C:226 , TYR C:227 , CL C:1303 , HOH C:1534 , HIS D:317
BINDING SITE FOR RESIDUE EDO C 1309
16
DC4
SOFTWARE
TYR D:93 , GLN D:167 , LLP D:193 , TYR D:318 , HOH D:1386 , HOH D:1611
BINDING SITE FOR RESIDUE EDO D 1312
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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PROSITE Patterns/Profiles
(, 0)
Info
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;
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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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2ogea_ (A:)
1b: SCOP_d2ogeb_ (B:)
1c: SCOP_d2ogec_ (C:)
1d: SCOP_d2oged_ (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
d2ogea_
A:
1b
d2ogeb_
B:
1c
d2ogec_
C:
1d
d2oged_
D:
[
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2ogeA01 (A:8-110,A:117-252)
1b: CATH_2ogeB01 (B:8-110,B:117-252)
1c: CATH_2ogeC01 (C:8-110,C:117-252)
1d: CATH_2ogeD01 (D:8-110,D:117-252)
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Topologies
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
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
2ogeA01
A:8-110,A:117-252
1b
2ogeB01
B:8-110,B:117-252
1c
2ogeC01
C:8-110,C:117-252
1d
2ogeD01
D:8-110,D:117-252
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Atom Selection
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Protein & NOT Site
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Chain C
Chain D
Asymmetric Unit 1
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Asym.Unit (264 KB)
Header - Asym.Unit
Biol.Unit 1 (131 KB)
Header - Biol.Unit 1
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