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1GKR
Asym. Unit
Info
Asym.Unit (294 KB)
Biol.Unit 1 (287 KB)
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(1)
Title
:
L-HYDANTOINASE (DIHYDROPYRIMIDINASE) FROM ARTHROBACTER AURESCENS
Authors
:
J. Abendroth, K. Niefind, D. Schomburg
Date
:
20 Aug 01 (Deposition) - 25 Jul 02 (Release) - 01 Sep 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Hydrolase, Hydantoinase, Dihydropyrimidinase, Cyclic Amidase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Abendroth, K. Niefind, O. May, M. Siemann, C. Syldatk, D. Schomburg
The Structure Of L-Hydantoinase From Arthobacter Aurescens Leads To An Understanding Of Dihydropyrimidinase Substrate And Enantio Specificity.
Biochemistry V. 41 8589 2002
(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
(12, 12)
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: ASA (AUTHOR)
10: ASB (AUTHOR)
11: ASC (AUTHOR)
12: ASD (AUTHOR)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
KCX A:147 , HIS A:183 , HIS A:239 , ZN A:1453 , HOH A:2124
BINDING SITE FOR RESIDUE ZN A1452
02
AC2
SOFTWARE
HIS A:60 , HIS A:62 , KCX A:147 , ASP A:312 , ZN A:1452 , HOH A:2124
BINDING SITE FOR RESIDUE ZN A1453
03
AC3
SOFTWARE
KCX B:147 , HIS B:183 , HIS B:239 , ZN B:1453 , HOH B:2129
BINDING SITE FOR RESIDUE ZN B1452
04
AC4
SOFTWARE
HIS B:60 , HIS B:62 , KCX B:147 , ASP B:312 , ZN B:1452 , HOH B:2129
BINDING SITE FOR RESIDUE ZN B1453
05
AC5
SOFTWARE
KCX C:147 , HIS C:183 , HIS C:239 , ZN C:1453 , HOH C:2128
BINDING SITE FOR RESIDUE ZN C1452
06
AC6
SOFTWARE
HIS C:60 , HIS C:62 , KCX C:147 , ASP C:312 , ZN C:1452 , HOH C:2128
BINDING SITE FOR RESIDUE ZN C1453
07
AC7
SOFTWARE
KCX D:147 , HIS D:183 , HIS D:239 , ZN D:1453 , HOH D:2127
BINDING SITE FOR RESIDUE ZN D1452
08
AC8
SOFTWARE
HIS D:60 , HIS D:62 , KCX D:147 , ASP D:312 , ZN D:1452 , HOH D:2127
BINDING SITE FOR RESIDUE ZN D1453
09
ASA
AUTHOR
HIS A:60 , HIS A:62 , KCX A:147 , HIS A:183 , HIS A:239 , ASP A:312 , HOH A:2124
CHAIN A COORDINATION OF THE TWO ZINC 2+ METALLOCENTE. THE METALLOCENTER IS BRIDGED BY KCX AND HOH. ZN1452---HOH1---ZN1453
10
ASB
AUTHOR
HIS B:60 , HIS B:62 , KCX B:147 , HIS B:183 , HIS B:239 , ASP B:312 , HOH B:2129
CHAIN B COORDINATION OF THE TWO ZINC 2+ METALLOCENTE. THE METALLOCENTER IS BRIDGED BY KCX AND HOH. ZN1452---HOH1---ZN1453
11
ASC
AUTHOR
HIS C:60 , HIS C:62 , KCX C:147 , HIS C:183 , HIS C:239 , ASP C:312 , HOH C:2128
CHAIN C COORDINATION OF THE TWO ZINC 2+ METALLOCENTE. THE METALLOCENTER IS BRIDGED BY KCX AND HOH. ZN1452---HOH1---ZN1453
12
ASD
AUTHOR
HIS D:60 , HIS D:62 , KCX D:147 , HIS D:183 , HIS D:239 , ASP D:312 , HOH D:2127
CHAIN D COORDINATION OF THE TWO ZINC 2+ METALLOCENTE. THE METALLOCENTER IS BRIDGED BY KCX AND HOH. ZN1452---HOH1---ZN1453
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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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;
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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_d1gkra1 (A:1-54,A:380-451)
1b: SCOP_d1gkrb1 (B:1-54,B:380-451)
1c: SCOP_d1gkrc1 (C:1-54,C:380-451)
1d: SCOP_d1gkrd1 (D:1-54,D:380-451)
2a: SCOP_d1gkra2 (A:55-379)
2b: SCOP_d1gkrb2 (B:55-379)
2c: SCOP_d1gkrc2 (C:55-379)
2d: SCOP_d1gkrd2 (D:55-379)
View:
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Classes
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)
(
)
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
:
L-hydantoinase
(1)
Arthrobacter aurescens [TaxId: 43663]
(1)
1a
d1gkra1
A:1-54,A:380-451
1b
d1gkrb1
B:1-54,B:380-451
1c
d1gkrc1
C:1-54,C:380-451
1d
d1gkrd1
D:1-54,D:380-451
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
:
L-hydantoinase
(1)
Arthrobacter aurescens [TaxId: 43663]
(1)
2a
d1gkra2
A:55-379
2b
d1gkrb2
B:55-379
2c
d1gkrc2
C:55-379
2d
d1gkrd2
D:55-379
[
close SCOP info
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1gkrB02 (B:55-375)
1b: CATH_1gkrA02 (A:54-373,A:393-419)
1c: CATH_1gkrC02 (C:54-373,C:393-419)
1d: CATH_1gkrD02 (D:54-373,D:393-419)
2a: CATH_1gkrB01 (B:1-54,B:376-451)
2b: CATH_1gkrA01 (A:1-53,A:381-392,A:420-441)
2c: CATH_1gkrC01 (C:1-53,C:381-392,C:420-441)
2d: CATH_1gkrD01 (D:1-53,D:381-392,D:420-441)
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(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Metal-dependent hydrolases
(190)
Arthrobacter aurescens. Organism_taxid: 43663.
(1)
1a
1gkrB02
B:55-375
1b
1gkrA02
A:54-373,A:393-419
1c
1gkrC02
C:54-373,C:393-419
1d
1gkrD02
D:54-373,D:393-419
Class
:
Mainly Beta
(13760)
Architecture
:
Roll
(1513)
Topology
:
Urease, subunit C; domain 1
(95)
Homologous Superfamily
:
Urease, subunit C, domain 1
(95)
Arthrobacter aurescens. Organism_taxid: 43663.
(1)
2a
1gkrB01
B:1-54,B:376-451
2b
1gkrA01
A:1-53,A:381-392,A:420-441
2c
1gkrC01
C:1-53,C:381-392,C:420-441
2d
1gkrD01
D:1-53,D:381-392,D:420-441
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Asymmetric Unit 1
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