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1K1D
Biol. Unit 2
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:
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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
(1, 4)
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
4
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
2
ZN
-1
Ligand/Ion
ZINC ION
[
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Sites
(8, 8)
Info
All Sites
1: AC5 (SOFTWARE)
2: AC6 (SOFTWARE)
3: AC7 (SOFTWARE)
4: AC8 (SOFTWARE)
5: AC9 (SOFTWARE)
6: BC1 (SOFTWARE)
7: BC2 (SOFTWARE)
8: BC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC5
SOFTWARE
KCX C:150 , HIS C:183 , HIS C:239 , ZN C:502
BINDING SITE FOR RESIDUE ZN C 501
2
AC6
SOFTWARE
HIS C:58 , HIS C:60 , KCX C:150 , ASP C:315 , ZN C:501
BINDING SITE FOR RESIDUE ZN C 502
3
AC7
SOFTWARE
KCX D:150 , HIS D:183 , HIS D:239 , ZN D:502
BINDING SITE FOR RESIDUE ZN D 501
4
AC8
SOFTWARE
HIS D:58 , HIS D:60 , KCX D:150 , ASP D:315 , ZN D:501
BINDING SITE FOR RESIDUE ZN D 502
5
AC9
SOFTWARE
KCX E:150 , HIS E:183 , HIS E:239 , ZN E:502
BINDING SITE FOR RESIDUE ZN E 501
6
BC1
SOFTWARE
HIS E:58 , HIS E:60 , KCX E:150 , ASP E:315 , ZN E:501
BINDING SITE FOR RESIDUE ZN E 502
7
BC2
SOFTWARE
KCX F:150 , HIS F:183 , HIS F:239 , ZN F:502
BINDING SITE FOR RESIDUE ZN F 501
8
BC3
SOFTWARE
HIS F:58 , HIS F:60 , KCX F:150 , ASP F:315 , ZN F:501
BINDING SITE FOR RESIDUE ZN F 502
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
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Exons
(0, 0)
Info
All Exons
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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.
(no "Exon" information available for biological units yet)
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)
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)
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)
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)
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)
(
)
Families
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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
:
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
[
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]
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)
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)
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)
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)
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
[
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]
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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)
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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