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1NFG
Asym. Unit
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Asym.Unit (300 KB)
Biol.Unit 1 (294 KB)
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(1)
Title
:
STRUCTURE OF D-HYDANTOINASE
Authors
:
Z. Xu, Y. Yang, W. Jiang, E. Arnold, J. Ding
Date
:
14 Dec 02 (Deposition) - 15 Jul 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Tim Barrel, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Z. Xu, Y. Liu, Y. Yang, W. Jiang, E. Arnold, J. Ding
Crystal Structure Of D-Hydantoinase From Burkholderia Pickettii At A Resolution Of 2. 7 Angstroms: Insights Into The Molecular Basis Of Enzyme Thermostability.
J. Bacteriol. V. 185 4038 2003
(for further references see the
PDB file header
)
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Hetero Components
(2, 12)
Info
All Hetero Components
1a: LYSINE NZ-CARBOXYLIC ACID (KCXa)
1b: LYSINE NZ-CARBOXYLIC ACID (KCXb)
1c: LYSINE NZ-CARBOXYLIC ACID (KCXc)
1d: LYSINE NZ-CARBOXYLIC ACID (KCXd)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
2e: ZINC ION (ZNe)
2f: ZINC ION (ZNf)
2g: ZINC ION (ZNg)
2h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
KCX
4
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
2
ZN
8
Ligand/Ion
ZINC ION
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:57 , HIS A:59 , KCX A:148 , ASP A:313 , ZN A:502
BINDING SITE FOR RESIDUE ZN A 501
2
AC2
SOFTWARE
KCX A:148 , HIS A:181 , HIS A:237 , ZN A:501 , HOH A:579
BINDING SITE FOR RESIDUE ZN A 502
3
AC3
SOFTWARE
HIS B:57 , HIS B:59 , KCX B:148 , ASP B:313 , ZN B:602
BINDING SITE FOR RESIDUE ZN B 601
4
AC4
SOFTWARE
KCX B:148 , HIS B:181 , HIS B:237 , ZN B:601 , HOH B:689
BINDING SITE FOR RESIDUE ZN B 602
5
AC5
SOFTWARE
HIS C:57 , HIS C:59 , KCX C:148 , ASP C:313 , ZN C:702
BINDING SITE FOR RESIDUE ZN C 701
6
AC6
SOFTWARE
KCX C:148 , HIS C:181 , HIS C:237 , ZN C:701 , HOH C:782
BINDING SITE FOR RESIDUE ZN C 702
7
AC7
SOFTWARE
HIS D:57 , HIS D:59 , KCX D:148 , ASP D:313 , ZN D:802
BINDING SITE FOR RESIDUE ZN D 801
8
AC8
SOFTWARE
KCX D:148 , HIS D:181 , HIS D:237 , ZN D:801 , HOH D:3085
BINDING SITE FOR RESIDUE ZN D 802
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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Exons
(0, 0)
Info
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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_d1nfga1 (A:1-51,A:382-457)
1b: SCOP_d1nfgb1 (B:1-51,B:382-457)
1c: SCOP_d1nfgc1 (C:1-51,C:382-457)
1d: SCOP_d1nfgd1 (D:1-51,D:382-457)
2a: SCOP_d1nfga2 (A:52-381)
2b: SCOP_d1nfgb2 (B:52-381)
2c: SCOP_d1nfgc2 (C:52-381)
2d: SCOP_d1nfgd2 (D:52-381)
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)
(
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(
)
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)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Composite domain of metallo-dependent hydrolases
(103)
Superfamily
:
Composite domain of metallo-dependent hydrolases
(103)
Family
:
Hydantoinase (dihydropyrimidinase)
(13)
Protein domain
:
D-hydantoinase
(5)
Burkholderia pickettii [TaxId: 329]
(1)
1a
d1nfga1
A:1-51,A:382-457
1b
d1nfgb1
B:1-51,B:382-457
1c
d1nfgc1
C:1-51,C:382-457
1d
d1nfgd1
D:1-51,D:382-457
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Metallo-dependent hydrolases
(273)
Family
:
Hydantoinase (dihydropyrimidinase), catalytic domain
(13)
Protein domain
:
D-hydantoinase
(5)
Burkholderia pickettii [TaxId: 329]
(1)
2a
d1nfga2
A:52-381
2b
d1nfgb2
B:52-381
2c
d1nfgc2
C:52-381
2d
d1nfgd2
D:52-381
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1nfgA02 (A:52-374,A:395-421)
1b: CATH_1nfgC02 (C:52-374,C:395-421)
1c: CATH_1nfgD02 (D:52-374,D:395-421)
1d: CATH_1nfgB02 (B:52-421)
2a: CATH_1nfgA01 (A:1-51,A:378-394,A:422-442)
2b: CATH_1nfgC01 (C:1-51,C:378-394,C:422-442)
2c: CATH_1nfgD01 (D:1-51,D:378-394,D:422-442)
2d: CATH_1nfgB01 (B:1-51,B:422-457)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Metal-dependent hydrolases
(190)
Ralstonia pickettii. Organism_taxid: 329.
(1)
1a
1nfgA02
A:52-374,A:395-421
1b
1nfgC02
C:52-374,C:395-421
1c
1nfgD02
D:52-374,D:395-421
1d
1nfgB02
B:52-421
Class
:
Mainly Beta
(13760)
Architecture
:
Roll
(1513)
Topology
:
Urease, subunit C; domain 1
(95)
Homologous Superfamily
:
Urease, subunit C, domain 1
(95)
Ralstonia pickettii. Organism_taxid: 329.
(1)
2a
1nfgA01
A:1-51,A:378-394,A:422-442
2b
1nfgC01
C:1-51,C:378-394,C:422-442
2c
1nfgD01
D:1-51,D:378-394,D:422-442
2d
1nfgB01
B:1-51,B:422-457
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Asymmetric Unit 1
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