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1K1D
Asym. Unit
Info
Asym.Unit (580 KB)
Biol.Unit 1 (290 KB)
Biol.Unit 2 (290 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF D-HYDANTOINASE
Authors
:
Y. H. Cheon, H. S. Kim, K. H. Han, J. Abendroth, K. Niefind, D. Schomburg, J. Wang, Y. Kim
Date
:
25 Sep 01 (Deposition) - 14 Aug 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.01
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,G,H (1x)
Biol. Unit 2: C,D,E,F (1x)
Keywords
:
D-Hydantoinase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. H. Cheon, H. S. Kim, K. H. Han, J. Abendroth, K. Niefind, D. Schomburg, J. Wang, Y. Kim
Crystal Structure Of D-Hydantoinase From Bacillus Stearothermophilus: Insight Into The Stereochemistry Of Enantioselectivity.
Biochemistry V. 41 9410 2002
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 24)
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)
1e: LYSINE NZ-CARBOXYLIC ACID (KCXe)
1f: LYSINE NZ-CARBOXYLIC ACID (KCXf)
1g: LYSINE NZ-CARBOXYLIC ACID (KCXg)
1h: LYSINE NZ-CARBOXYLIC ACID (KCXh)
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)
2i: ZINC ION (ZNi)
2j: ZINC ION (ZNj)
2k: ZINC ION (ZNk)
2l: ZINC ION (ZNl)
2m: ZINC ION (ZNm)
2n: ZINC ION (ZNn)
2o: ZINC ION (ZNo)
2p: ZINC ION (ZNp)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
KCX
8
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
2
ZN
16
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(16, 16)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
KCX A:150 , HIS A:183 , HIS A:239 , ZN A:502
BINDING SITE FOR RESIDUE ZN A 501
02
AC2
SOFTWARE
HIS A:58 , HIS A:60 , KCX A:150 , ASP A:315 , ZN A:501
BINDING SITE FOR RESIDUE ZN A 502
03
AC3
SOFTWARE
KCX B:150 , HIS B:183 , HIS B:239 , ZN B:502
BINDING SITE FOR RESIDUE ZN B 501
04
AC4
SOFTWARE
HIS B:58 , HIS B:60 , KCX B:150 , ASP B:315 , ZN B:501
BINDING SITE FOR RESIDUE ZN B 502
05
AC5
SOFTWARE
KCX C:150 , HIS C:183 , HIS C:239 , ZN C:502
BINDING SITE FOR RESIDUE ZN C 501
06
AC6
SOFTWARE
HIS C:58 , HIS C:60 , KCX C:150 , ASP C:315 , ZN C:501
BINDING SITE FOR RESIDUE ZN C 502
07
AC7
SOFTWARE
KCX D:150 , HIS D:183 , HIS D:239 , ZN D:502
BINDING SITE FOR RESIDUE ZN D 501
08
AC8
SOFTWARE
HIS D:58 , HIS D:60 , KCX D:150 , ASP D:315 , ZN D:501
BINDING SITE FOR RESIDUE ZN D 502
09
AC9
SOFTWARE
KCX E:150 , HIS E:183 , HIS E:239 , ZN E:502
BINDING SITE FOR RESIDUE ZN E 501
10
BC1
SOFTWARE
HIS E:58 , HIS E:60 , KCX E:150 , ASP E:315 , ZN E:501
BINDING SITE FOR RESIDUE ZN E 502
11
BC2
SOFTWARE
KCX F:150 , HIS F:183 , HIS F:239 , ZN F:502
BINDING SITE FOR RESIDUE ZN F 501
12
BC3
SOFTWARE
HIS F:58 , HIS F:60 , KCX F:150 , ASP F:315 , ZN F:501
BINDING SITE FOR RESIDUE ZN F 502
13
BC4
SOFTWARE
KCX G:150 , HIS G:183 , HIS G:239 , ZN G:502
BINDING SITE FOR RESIDUE ZN G 501
14
BC5
SOFTWARE
HIS G:58 , HIS G:60 , KCX G:150 , ASP G:315 , ZN G:501
BINDING SITE FOR RESIDUE ZN G 502
15
BC6
SOFTWARE
KCX H:150 , HIS H:183 , HIS H:239 , ZN H:502
BINDING SITE FOR RESIDUE ZN H 501
16
BC7
SOFTWARE
HIS H:58 , HIS H:60 , KCX H:150 , ASP H:315 , ZN H:501
BINDING SITE FOR RESIDUE ZN H 502
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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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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Label:
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
(2, 16)
Info
All SCOP Domains
1a: SCOP_d1k1da1 (A:1-52,A:385-460)
1b: SCOP_d1k1db1 (B:1-52,B:385-460)
1c: SCOP_d1k1dc1 (C:1-52,C:385-460)
1d: SCOP_d1k1dd1 (D:1-52,D:385-460)
1e: SCOP_d1k1de1 (E:1-52,E:385-460)
1f: SCOP_d1k1df1 (F:1-52,F:385-460)
1g: SCOP_d1k1dg1 (G:1-52,G:385-460)
1h: SCOP_d1k1dh1 (H:1-52,H:385-460)
2a: SCOP_d1k1da2 (A:53-384)
2b: SCOP_d1k1db2 (B:53-384)
2c: SCOP_d1k1dc2 (C:53-384)
2d: SCOP_d1k1dd2 (D:53-384)
2e: SCOP_d1k1de2 (E:53-384)
2f: SCOP_d1k1df2 (F:53-384)
2g: SCOP_d1k1dg2 (G:53-384)
2h: SCOP_d1k1dh2 (H:53-384)
View:
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Classes
(
)
(
)
Folds
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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)
Bacillus stearothermophilus [TaxId: 1422]
(1)
1a
d1k1da1
A:1-52,A:385-460
1b
d1k1db1
B:1-52,B:385-460
1c
d1k1dc1
C:1-52,C:385-460
1d
d1k1dd1
D:1-52,D:385-460
1e
d1k1de1
E:1-52,E:385-460
1f
d1k1df1
F:1-52,F:385-460
1g
d1k1dg1
G:1-52,G:385-460
1h
d1k1dh1
H:1-52,H:385-460
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)
Bacillus stearothermophilus [TaxId: 1422]
(1)
2a
d1k1da2
A:53-384
2b
d1k1db2
B:53-384
2c
d1k1dc2
C:53-384
2d
d1k1dd2
D:53-384
2e
d1k1de2
E:53-384
2f
d1k1df2
F:53-384
2g
d1k1dg2
G:53-384
2h
d1k1dh2
H:53-384
[
close SCOP info
]
CATH Domains
(2, 16)
Info
all CATH domains
1a: CATH_1k1dA02 (A:53-380)
1b: CATH_1k1dB02 (B:53-380)
1c: CATH_1k1dC02 (C:53-380)
1d: CATH_1k1dD02 (D:53-380)
1e: CATH_1k1dE02 (E:53-380)
1f: CATH_1k1dF02 (F:53-380)
1g: CATH_1k1dG02 (G:53-380)
1h: CATH_1k1dH02 (H:53-380)
2a: CATH_1k1dA01 (A:1-52,A:381-460)
2b: CATH_1k1dB01 (B:1-52,B:381-460)
2c: CATH_1k1dC01 (C:1-52,C:381-460)
2d: CATH_1k1dD01 (D:1-52,D:381-460)
2e: CATH_1k1dE01 (E:1-52,E:381-460)
2f: CATH_1k1dF01 (F:1-52,F:381-460)
2g: CATH_1k1dG01 (G:1-52,G:381-460)
2h: CATH_1k1dH01 (H:1-52,H:381-460)
View:
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Topologies
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Metal-dependent hydrolases
(190)
Geobacillus stearothermophilus. Organism_taxid: 1422.
(1)
1a
1k1dA02
A:53-380
1b
1k1dB02
B:53-380
1c
1k1dC02
C:53-380
1d
1k1dD02
D:53-380
1e
1k1dE02
E:53-380
1f
1k1dF02
F:53-380
1g
1k1dG02
G:53-380
1h
1k1dH02
H:53-380
Class
:
Mainly Beta
(13760)
Architecture
:
Roll
(1513)
Topology
:
Urease, subunit C; domain 1
(95)
Homologous Superfamily
:
Urease, subunit C, domain 1
(95)
Geobacillus stearothermophilus. Organism_taxid: 1422.
(1)
2a
1k1dA01
A:1-52,A:381-460
2b
1k1dB01
B:1-52,B:381-460
2c
1k1dC01
C:1-52,C:381-460
2d
1k1dD01
D:1-52,D:381-460
2e
1k1dE01
E:1-52,E:381-460
2f
1k1dF01
F:1-52,F:381-460
2g
1k1dG01
G:1-52,G:381-460
2h
1k1dH01
H:1-52,H:381-460
[
close CATH info
]
Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_Amidohydro_4_1k1dH01 (H:44-394)
1b: PFAM_Amidohydro_4_1k1dH02 (H:44-394)
1c: PFAM_Amidohydro_4_1k1dH03 (H:44-394)
1d: PFAM_Amidohydro_4_1k1dH04 (H:44-394)
1e: PFAM_Amidohydro_4_1k1dH05 (H:44-394)
1f: PFAM_Amidohydro_4_1k1dH06 (H:44-394)
1g: PFAM_Amidohydro_4_1k1dH07 (H:44-394)
1h: PFAM_Amidohydro_4_1k1dH08 (H:44-394)
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(
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(
)
(
)
Clan
:
Amidohydrolase
(126)
Family
:
Amidohydro_4
(8)
Geobacillus stearothermophilus (Bacillus stearothermophilus)
(1)
1a
Amidohydro_4-1k1dH01
H:44-394
1b
Amidohydro_4-1k1dH02
H:44-394
1c
Amidohydro_4-1k1dH03
H:44-394
1d
Amidohydro_4-1k1dH04
H:44-394
1e
Amidohydro_4-1k1dH05
H:44-394
1f
Amidohydro_4-1k1dH06
H:44-394
1g
Amidohydro_4-1k1dH07
H:44-394
1h
Amidohydro_4-1k1dH08
H:44-394
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