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3B8X
Asym. Unit
Info
Asym.Unit (150 KB)
Biol.Unit 1 (144 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF GDP-4-KETO-6-DEOXYMANNOSE-3-DEHYDRATASE (COLD) H188N MUTANT WITH BOUND GDP-PEROSAMINE
Authors
:
P. D. Cook, H. M. Holden
Date
:
02 Nov 07 (Deposition) - 27 Nov 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Aspartate Aminotransferase, Colitose, Perosamine, O-Antigen, Plp, Pyridoxal Phosphate, , Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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Reference
:
P. D. Cook, H. M. Holden
Gdp-4-Keto-6-Deoxy-D-Mannose 3-Dehydratase, Accommodating A Sugar Substrate In The Active Site.
J. Biol. Chem. V. 283 4295 2008
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Hetero Components
(3, 13)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
2a: [(2R,3S,4R,5R)-5-(2-AMINO-6-OXO-1,... (G4Ma)
2b: [(2R,3S,4R,5R)-5-(2-AMINO-6-OXO-1,... (G4Mb)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
3c: SODIUM ION (NAc)
3d: SODIUM ION (NAd)
3e: SODIUM ION (NAe)
3f: SODIUM ION (NAf)
3g: SODIUM ION (NAg)
3h: SODIUM ION (NAh)
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No.
Name
Count
Type
Full Name
1
EDO
3
Ligand/Ion
1,2-ETHANEDIOL
2
G4M
2
Ligand/Ion
[(2R,3S,4R,5R)-5-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL (2R,3S,4S,5S,6R)-3,4-DIHYDROXY-5-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]-6-METHYLTETRAHYDRO-2H-PYRAN-2-YL DIHYDROGEN DIPHOSPHATE
3
NA
8
Ligand/Ion
SODIUM ION
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Sites
(13, 13)
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)
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:175 , ASP A:201 , HOH A:688 , HOH A:751 , HOH B:717 , HOH B:747
BINDING SITE FOR RESIDUE NA A 669
02
AC2
SOFTWARE
LEU A:6 , ASN A:371 , HOH A:743 , HOH A:744 , HOH A:872
BINDING SITE FOR RESIDUE NA A 671
03
AC3
SOFTWARE
GLU A:80 , LYS A:103 , ALA A:122 , THR A:124 , SER A:126 , THR A:127
BINDING SITE FOR RESIDUE NA A 672
04
AC4
SOFTWARE
THR A:10 , ASN A:188 , ARG A:273 , GLN A:373 , HOH A:831 , HOH A:853
BINDING SITE FOR RESIDUE NA A 673
05
AC5
SOFTWARE
LEU B:6 , ASN B:371 , HOH B:694 , HOH B:722 , HOH B:745 , HOH B:751
BINDING SITE FOR RESIDUE NA B 666
06
AC6
SOFTWARE
GLU B:375 , ASP B:378 , HOH B:847 , HOH B:912 , HOH B:995 , HOH B:997 , HOH B:1000
BINDING SITE FOR RESIDUE NA B 667
07
AC7
SOFTWARE
PHE A:242 , ASN B:341 , ASP B:343 , HOH B:895 , HOH B:959
BINDING SITE FOR RESIDUE NA B 668
08
AC8
SOFTWARE
THR B:175 , ASP B:201 , HOH B:765 , HOH B:798 , HOH B:859 , HOH B:892
BINDING SITE FOR RESIDUE NA B 670
09
AC9
SOFTWARE
SER A:55 , GLY A:56 , SER A:57 , ASN A:60 , SER A:87 , TRP A:88 , THR A:91 , ASP A:159 , CYS A:161 , GLU A:162 , SER A:183 , PHE A:185 , TYR A:186 , SER A:187 , GLU A:329 , ARG A:331 , HOH A:677 , HOH A:756 , HOH A:817 , HOH A:885 , HOH A:914 , LYS B:26 , MET B:27 , PHE B:28 , THR B:29 , HIS B:215 , ARG B:219 , PHE B:240 , ASN B:248 , HOH B:903
BINDING SITE FOR RESIDUE G4M A 500
10
BC1
SOFTWARE
GLU A:38 , ALA A:50 , TYR A:206 , HOH A:811
BINDING SITE FOR RESIDUE EDO A 674
11
BC2
SOFTWARE
SER A:9 , THR A:10 , TRP A:11 , ARG A:268 , GLN A:373
BINDING SITE FOR RESIDUE EDO A 675
12
BC3
SOFTWARE
GLY A:78 , GLU A:80 , ARG A:101
BINDING SITE FOR RESIDUE EDO A 676
13
BC4
SOFTWARE
LYS A:26 , MET A:27 , PHE A:28 , THR A:29 , HIS A:215 , ARG A:219 , PHE A:240 , ASN A:248 , LEU B:6 , SER B:55 , GLY B:56 , SER B:57 , TRP B:88 , THR B:90 , ASP B:159 , CYS B:161 , GLU B:162 , SER B:183 , PHE B:185 , TYR B:186 , SER B:187 , GLU B:329 , ARG B:331 , HOH B:676 , HOH B:705 , HOH B:742 , HOH B:761 , HOH B:864 , HOH B:866 , HOH B:925
BINDING SITE FOR RESIDUE G4M B 500
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_3b8xA01 (A:3-264)
1b: CATH_3b8xB01 (B:1-264)
2a: CATH_3b8xA02 (A:265-388)
2b: CATH_3b8xB02 (B:265-388)
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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)
Escherichia coli o55:h7. Organism_taxid: 244320. Strain: o55:h7.
(1)
1a
3b8xA01
A:3-264
1b
3b8xB01
B:1-264
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Aspartate Aminotransferase, domain 1
(355)
Homologous Superfamily
:
Aspartate Aminotransferase, domain 1
(354)
Escherichia coli o55:h7. Organism_taxid: 244320. Strain: o55:h7.
(1)
2a
3b8xA02
A:265-388
2b
3b8xB02
B:265-388
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Pfam Domains
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Asymmetric Unit 1
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