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4G3M
Asym. Unit
Info
Asym.Unit (238 KB)
Biol.Unit 1 (232 KB)
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(1)
Title
:
COMPLEX STRUCTURE OF BACILLUS SUBTILIS RIBG: THE DEAMINATION PROCESS IN RIBOFLAVIN BIOSYNTHESIS
Authors
:
S. C. Chen, C. Y. Shen, T. M. Yen, H. C. Yu, T. H. Chang, W. L. Lai, S. H. Liaw
Date
:
15 Jul 12 (Deposition) - 20 Feb 13 (Release) - 20 Feb 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.56
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Alpha/Beta/Alpha, Deaminase Domain, Reductase Domain, Hydrolase, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. C. Chen, C. Y. Shen, T. M. Yen, H. C. Yu, T. H. Chang, W. L. Lai, S. H. Liaw
Evolution Of Vitamin B(2) Biosynthesis: Eubacterial Ribg An Fungal Rib2 Deaminases.
Acta Crystallogr. , Sect. D V. 69 227 2013
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Hetero Components
(3, 11)
Info
All Hetero Components
1a: [(2R,3S,4S,5E)-5-[[5-AZANYL-2,4-BI... (AI9a)
1b: [(2R,3S,4S,5E)-5-[[5-AZANYL-2,4-BI... (AI9b)
1c: [(2R,3S,4S,5E)-5-[[5-AZANYL-2,4-BI... (AI9c)
1d: [(2R,3S,4S,5E)-5-[[5-AZANYL-2,4-BI... (AI9d)
2a: N-(5-AMINO-2,6-DIOXO-1,2,3,6-TETRA... (AOFa)
2b: N-(5-AMINO-2,6-DIOXO-1,2,3,6-TETRA... (AOFb)
2c: N-(5-AMINO-2,6-DIOXO-1,2,3,6-TETRA... (AOFc)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AI9
4
Ligand/Ion
[(2R,3S,4S,5E)-5-[[5-AZANYL-2,4-BIS(OXIDANYLIDENE)-1H-PYRIMIDIN-6-YL]IMINO]-2,3,4-TRIS(OXIDANYL)PENTYL]DIHYDROGEN PHOSPHATE
2
AOF
3
Ligand/Ion
N-(5-AMINO-2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDIN-4-YL)-5-O-PHOSPHONO-BETA-D-RIBOFURANOSYLAMINE
3
ZN
4
Ligand/Ion
ZINC ION
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Sites
(11, 11)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:49 , GLU A:51 , CYS A:74 , CYS A:83
BINDING SITE FOR RESIDUE ZN A 401
02
AC2
SOFTWARE
LYS A:151 , ALA A:153 , SER A:167 , ILE A:170 , THR A:171 , ARG A:176 , ARG A:183 , ASP A:199 , PRO A:201 , SER A:202 , LEU A:203 , THR A:204 , ARG A:206 , GLU A:290 , HOH A:511 , HOH A:546 , HOH A:603
BINDING SITE FOR RESIDUE AI9 A 402
03
AC3
SOFTWARE
HIS B:49 , CYS B:74 , CYS B:83 , AOF B:402
BINDING SITE FOR RESIDUE ZN B 401
04
AC4
SOFTWARE
ASN B:23 , VAL B:26 , HIS B:42 , HIS B:49 , ALA B:50 , GLU B:51 , CYS B:74 , HIS B:76 , LYS B:79 , THR B:80 , CYS B:83 , ASP B:101 , ASN B:103 , PHE B:137 , ZN B:401 , HOH B:503 , HOH B:533
BINDING SITE FOR RESIDUE AOF B 402
05
AC5
SOFTWARE
LYS B:151 , ALA B:153 , SER B:167 , ILE B:170 , THR B:171 , ARG B:176 , ARG B:183 , ASP B:199 , PRO B:201 , SER B:202 , LEU B:203 , ARG B:206 , HOH B:568
BINDING SITE FOR RESIDUE AI9 B 403
06
AC6
SOFTWARE
HIS C:49 , CYS C:74 , CYS C:83 , AOF C:402
BINDING SITE FOR RESIDUE ZN C 401
07
AC7
SOFTWARE
ASN C:23 , PRO C:24 , VAL C:26 , HIS C:42 , HIS C:49 , ALA C:50 , GLU C:51 , CYS C:74 , GLY C:78 , LYS C:79 , THR C:80 , ASP C:101 , PHE C:137 , ZN C:401 , HOH C:550 , HOH C:561
BINDING SITE FOR RESIDUE AOF C 402
08
AC8
SOFTWARE
LYS C:151 , ALA C:153 , SER C:167 , TRP C:169 , ILE C:170 , THR C:171 , ARG C:176 , ARG C:183 , ASP C:199 , PRO C:201 , SER C:202 , LEU C:203 , ARG C:206 , GLU C:290 , HOH C:506 , HOH C:549
BINDING SITE FOR RESIDUE AI9 C 403
09
AC9
SOFTWARE
HIS D:49 , CYS D:74 , CYS D:83 , AOF D:402
BINDING SITE FOR RESIDUE ZN D 401
10
BC1
SOFTWARE
ASN D:23 , PRO D:24 , VAL D:26 , HIS D:42 , HIS D:49 , ALA D:50 , GLU D:51 , CYS D:74 , HIS D:76 , GLY D:78 , LYS D:79 , THR D:80 , CYS D:83 , ASP D:101 , PHE D:137 , ZN D:401 , HOH D:530 , HOH D:549
BINDING SITE FOR RESIDUE AOF D 402
11
BC2
SOFTWARE
LYS D:151 , ALA D:153 , ILE D:170 , THR D:171 , ARG D:176 , ARG D:183 , ASP D:199 , PRO D:201 , SER D:202 , LEU D:203 , ARG D:206 , GLU D:290
BINDING SITE FOR RESIDUE AI9 D 403
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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Exons
(0, 0)
Info
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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.
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d4g3ma1 (A:0-145)
1b: SCOP_d4g3mb1 (B:-1-145)
1c: SCOP_d4g3mc1 (C:-1-145)
1d: SCOP_d4g3md1 (D:-1-145)
2a: SCOP_d4g3ma2 (A:146-360)
2b: SCOP_d4g3mb2 (B:146-359)
2c: SCOP_d4g3mc2 (C:146-359)
2d: SCOP_d4g3md2 (D:146-359)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Cytidine deaminase-like
(78)
Superfamily
:
Cytidine deaminase-like
(76)
Family
:
Deoxycytidylate deaminase-like
(29)
Protein domain
:
Riboflavin biosynthesis protein RibD
(5)
Bacillus subtilis [TaxId: 1423]
(4)
1a
d4g3ma1
A:0-145
1b
d4g3mb1
B:-1-145
1c
d4g3mc1
C:-1-145
1d
d4g3md1
D:-1-145
Fold
:
Dihydrofolate reductase-like
(332)
Superfamily
:
Dihydrofolate reductase-like
(332)
Family
:
RibD C-terminal domain-like
(7)
Protein domain
:
Riboflavin biosynthesis protein RibD
(5)
Bacillus subtilis [TaxId: 1423]
(4)
2a
d4g3ma2
A:146-360
2b
d4g3mb2
B:146-359
2c
d4g3mc2
C:146-359
2d
d4g3md2
D:146-359
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CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
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Sorry, no Info available
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Asymmetric Unit 1
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (238 KB)
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