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2OGE
Asym. Unit
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
(4, 35)
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
8
Ligand/Ion
CHLORIDE ION
2
EDO
21
Ligand/Ion
1,2-ETHANEDIOL
3
LLP
4
Mod. Amino Acid
2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
4
NA
2
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(31, 31)
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)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:39 , LEU A:40 , HOH A:1482 , HOH B:1450
BINDING SITE FOR RESIDUE CL A 1297
02
AC2
SOFTWARE
TYR A:227 , HIS A:229 , EDO A:1304 , HOH B:1313
BINDING SITE FOR RESIDUE CL A 1298
03
AC3
SOFTWARE
ASN A:65 , HOH A:1338 , ASN B:65 , HOH B:1308 , HOH B:1309 , HOH B:1454
BINDING SITE FOR RESIDUE NA A 1299
04
AC4
SOFTWARE
TYR B:39 , LEU B:40
BINDING SITE FOR RESIDUE CL B 1300
05
AC5
SOFTWARE
TYR A:318 , HOH A:1435 , HIS B:229 , EDO B:1304
BINDING SITE FOR RESIDUE CL B 1301
06
AC6
SOFTWARE
TYR C:39 , LEU C:40 , HOH C:1343
BINDING SITE FOR RESIDUE CL C 1302
07
AC7
SOFTWARE
TYR C:227 , HIS C:229 , EDO C:1309 , HOH C:1533 , TYR D:318
BINDING SITE FOR RESIDUE CL C 1303
08
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
09
AC9
SOFTWARE
TYR D:39 , LEU D:40
BINDING SITE FOR RESIDUE CL D 1305
10
BC1
SOFTWARE
TYR C:318 , HIS D:229
BINDING SITE FOR RESIDUE CL D 1306
11
BC2
SOFTWARE
PRO A:11 , PHE A:12 , LEU A:13 , ASP A:14 , ASP A:313 , HOH A:1309
BINDING SITE FOR RESIDUE EDO A 1300
12
BC3
SOFTWARE
TYR A:55 , GLU A:57 , ARG A:172 , ARG A:177
BINDING SITE FOR RESIDUE EDO A 1301
13
BC4
SOFTWARE
THR A:118 , PRO A:121 , ASP A:146 , HOH A:1361 , HOH A:1364 , HOH A:1529
BINDING SITE FOR RESIDUE EDO A 1302
14
BC5
SOFTWARE
PRO A:191 , LLP A:193 , ASN A:194 , GLY A:196 , ARG A:249 , HOH A:1313 , HOH A:1388 , HOH A:1389
BINDING SITE FOR RESIDUE EDO A 1303
15
BC6
SOFTWARE
TYR A:227 , HIS A:229 , CL A:1298 , TYR B:93
BINDING SITE FOR RESIDUE EDO A 1304
16
BC7
SOFTWARE
PRO B:11 , PHE B:12 , LEU B:13 , ASP B:313 , HOH B:1331
BINDING SITE FOR RESIDUE EDO B 1302
17
BC8
SOFTWARE
PRO B:191 , LLP B:193 , ASN B:194 , ARG B:249 , PRO B:355 , HOH B:1332 , HOH B:1410 , HOH B:1412
BINDING SITE FOR RESIDUE EDO B 1303
18
BC9
SOFTWARE
TYR A:93 , TYR A:190 , LLP A:193 , TYR B:221 , ASN B:235 , ARG B:237
BINDING SITE FOR RESIDUE EDO A 1305
19
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
20
CC2
SOFTWARE
ARG C:151 , ARG C:176 , ARG C:177 , HOH C:1404 , HOH C:1521
BINDING SITE FOR RESIDUE EDO C 1306
21
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
22
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
23
CC5
SOFTWARE
ASP C:27 , EDO C:1308 , ASP D:27
BINDING SITE FOR RESIDUE EDO C 1307
24
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
25
CC7
SOFTWARE
ASP A:27 , ALA A:31 , ASP B:27 , ILE B:30
BINDING SITE FOR RESIDUE EDO A 1306
26
CC8
SOFTWARE
LEU A:315 , HIS A:317 , LYS B:226 , TYR B:227 , CL B:1301 , HOH B:1451
BINDING SITE FOR RESIDUE EDO B 1304
27
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
28
DC1
SOFTWARE
ARG D:172 , ARG D:177 , HOH D:1534
BINDING SITE FOR RESIDUE EDO D 1311
29
DC2
SOFTWARE
ASP C:27 , ALA C:28 , EDO C:1307 , HOH C:1337
BINDING SITE FOR RESIDUE EDO C 1308
30
DC3
SOFTWARE
LYS C:226 , TYR C:227 , CL C:1303 , HOH C:1534 , HIS D:317
BINDING SITE FOR RESIDUE EDO C 1309
31
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 not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
View:
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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
(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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Classes
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)
(
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Folds
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(
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Superfamilies
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)
(
)
Families
(
)
(
)
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:
[
close SCOP info
]
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)
View:
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Architectures
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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
View:
Select:
Label:
Sorry, no Info available
[
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Atom Selection
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Asym.Unit (264 KB)
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