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1GKP
Asym. Unit
Info
Asym.Unit (1.0 MB)
Biol.Unit 1 (677 KB)
Biol.Unit 2 (681 KB)
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(1)
Title
:
D-HYDANTOINASE (DIHYDROPYRIMIDINASE) FROM THERMUS SP. IN SPACE GROUP C2221
Authors
:
J. Abendroth, K. Niefind, D. Schomburg
Date
:
20 Aug 01 (Deposition) - 27 Jun 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.29
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B (2x)
Biol. Unit 2: C,D,E,F (1x)
Keywords
:
Hydrolase, Hydantoinase, Dihydropyrimidinase, Cyclic Amidase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Abendroth, K. Niefind, D. Schomburg
X-Ray Structure Of A Dihydropyrimidinase From Thermus Sp. At 1. 3 A Resolution
J. Mol. Biol. V. 320 143 2002
(for further references see the
PDB file header
)
[
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Hetero Components
(4, 29)
Info
All Hetero Components
1a: 4-(2-HYDROXYETHYL)-1-PIPERAZINEETH... (EPEa)
1b: 4-(2-HYDROXYETHYL)-1-PIPERAZINEETH... (EPEb)
2a: LYSINE NZ-CARBOXYLIC ACID (KCXa)
2b: LYSINE NZ-CARBOXYLIC ACID (KCXb)
2c: LYSINE NZ-CARBOXYLIC ACID (KCXc)
2d: LYSINE NZ-CARBOXYLIC ACID (KCXd)
2e: LYSINE NZ-CARBOXYLIC ACID (KCXe)
2f: LYSINE NZ-CARBOXYLIC ACID (KCXf)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
3i: SULFATE ION (SO4i)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
4c: ZINC ION (ZNc)
4d: ZINC ION (ZNd)
4e: ZINC ION (ZNe)
4f: ZINC ION (ZNf)
4g: ZINC ION (ZNg)
4h: ZINC ION (ZNh)
4i: ZINC ION (ZNi)
4j: ZINC ION (ZNj)
4k: ZINC ION (ZNk)
4l: ZINC ION (ZNl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EPE
2
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
2
KCX
6
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
3
SO4
9
Ligand/Ion
SULFATE ION
4
ZN
12
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(23, 23)
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)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
KCX A:150 , HIS A:183 , HIS A:239 , ZN A:1461 , HOH A:2605 , HOH A:2606
BINDING SITE FOR RESIDUE ZN A1460
02
AC2
SOFTWARE
HIS A:59 , HIS A:61 , KCX A:150 , ASP A:315 , ZN A:1460 , HOH A:2606
BINDING SITE FOR RESIDUE ZN A1461
03
AC3
SOFTWARE
LYS A:370 , LYS A:373 , HOH A:2507 , HOH A:2508 , HOH A:2607 , HOH A:2608 , HOH A:2609 , HIS B:361 , ARG B:362
BINDING SITE FOR RESIDUE SO4 A1462
04
AC4
SOFTWARE
KCX B:150 , HIS B:183 , HIS B:239 , ZN B:1461 , HOH B:2584 , HOH B:2585
BINDING SITE FOR RESIDUE ZN B1460
05
AC5
SOFTWARE
HIS B:59 , HIS B:61 , KCX B:150 , ASP B:315 , ZN B:1460 , HOH B:2585
BINDING SITE FOR RESIDUE ZN B1461
06
AC6
SOFTWARE
HIS A:361 , LYS B:370 , LYS B:373 , HOH B:2472 , HOH B:2473 , HOH B:2586 , HOH B:2587 , HOH B:2588
BINDING SITE FOR RESIDUE SO4 B1462
07
AC7
SOFTWARE
KCX C:150 , HIS C:183 , HIS C:239 , ZN C:1461 , HOH C:2654 , HOH C:2655
BINDING SITE FOR RESIDUE ZN C1460
08
AC8
SOFTWARE
HIS C:59 , HIS C:61 , KCX C:150 , ASP C:315 , ZN C:1460 , HOH C:2655
BINDING SITE FOR RESIDUE ZN C1461
09
AC9
SOFTWARE
LYS C:370 , LYS C:373 , HOH C:2548 , HOH C:2549 , HOH C:2656 , HOH C:2657 , HOH C:2658 , HIS D:361 , ARG D:362
BINDING SITE FOR RESIDUE SO4 C1462
10
BC1
SOFTWARE
GLN C:107 , LYS C:110 , HOH C:2661 , HOH C:2662 , EPE F:1463
BINDING SITE FOR RESIDUE SO4 C1463
11
BC2
SOFTWARE
KCX D:150 , HIS D:183 , HIS D:239 , ZN D:1461 , HOH D:2555 , HOH D:2556
BINDING SITE FOR RESIDUE ZN D1460
12
BC3
SOFTWARE
HIS D:59 , HIS D:61 , KCX D:150 , ASP D:315 , ZN D:1460 , HOH D:2556
BINDING SITE FOR RESIDUE ZN D1461
13
BC4
SOFTWARE
HIS C:361 , LYS D:370 , LYS D:373 , HOH D:2456 , HOH D:2457 , HOH D:2557 , HOH D:2558 , HOH D:2559 , HOH D:2560
BINDING SITE FOR RESIDUE SO4 D1462
14
BC5
SOFTWARE
KCX E:150 , HIS E:183 , HIS E:239 , ZN E:1461 , HOH E:2680 , HOH E:2681
BINDING SITE FOR RESIDUE ZN E1460
15
BC6
SOFTWARE
HIS E:59 , HIS E:61 , KCX E:150 , ASP E:315 , ZN E:1460 , HOH E:2681
BINDING SITE FOR RESIDUE ZN E1461
16
BC7
SOFTWARE
LYS E:370 , LYS E:373 , HOH E:2555 , HOH E:2556 , HOH E:2682 , HOH E:2683 , HOH E:2685 , HOH E:2687 , HIS F:361
BINDING SITE FOR RESIDUE SO4 E1462
17
BC8
SOFTWARE
EPE D:1463 , GLN E:107 , LYS E:110 , HOH E:2688 , HOH E:2689
BINDING SITE FOR RESIDUE SO4 E1463
18
BC9
SOFTWARE
ARG E:438 , HOH E:2690 , HOH E:2691
BINDING SITE FOR RESIDUE SO4 E1464
19
CC1
SOFTWARE
KCX F:150 , HIS F:183 , HIS F:239 , ZN F:1461 , HOH F:2591 , HOH F:2592
BINDING SITE FOR RESIDUE ZN F1460
20
CC2
SOFTWARE
HIS F:59 , HIS F:61 , KCX F:150 , ASP F:315 , ZN F:1460 , HOH F:2592
BINDING SITE FOR RESIDUE ZN F1461
21
CC3
SOFTWARE
HIS E:361 , HOH E:2553 , LYS F:370 , LYS F:373 , HOH F:2483 , HOH F:2485 , HOH F:2594 , HOH F:2595 , HOH F:2596
BINDING SITE FOR RESIDUE SO4 F1462
22
CC4
SOFTWARE
VAL D:428 , ASP D:439 , HOH D:2524 , HOH D:2562 , HOH D:2563 , HOH D:2564 , GLN E:107 , GLU E:140 , SO4 E:1463
BINDING SITE FOR RESIDUE EPE D1463
23
CC5
SOFTWARE
LEU C:103 , GLN C:107 , GLU C:140 , SO4 C:1463 , SER F:427 , VAL F:428 , ASP F:439 , HOH F:2597 , HOH F:2598 , HOH F:2599 , HOH F:2600
BINDING SITE FOR RESIDUE EPE F1463
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(0, 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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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 12)
Info
All SCOP Domains
1a: SCOP_d1gkpa1 (A:2-54,A:390-459)
1b: SCOP_d1gkpb1 (B:2-54,B:390-459)
1c: SCOP_d1gkpc1 (C:2-54,C:390-459)
1d: SCOP_d1gkpd1 (D:2-54,D:390-459)
1e: SCOP_d1gkpe1 (E:2-54,E:390-459)
1f: SCOP_d1gkpf1 (F:2-54,F:390-459)
2a: SCOP_d1gkpa2 (A:55-389)
2b: SCOP_d1gkpb2 (B:55-389)
2c: SCOP_d1gkpc2 (C:55-389)
2d: SCOP_d1gkpd2 (D:55-389)
2e: SCOP_d1gkpe2 (E:55-389)
2f: SCOP_d1gkpf2 (F:55-389)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
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)
Thermus sp. [TaxId: 275]
(2)
1a
d1gkpa1
A:2-54,A:390-459
1b
d1gkpb1
B:2-54,B:390-459
1c
d1gkpc1
C:2-54,C:390-459
1d
d1gkpd1
D:2-54,D:390-459
1e
d1gkpe1
E:2-54,E:390-459
1f
d1gkpf1
F:2-54,F:390-459
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)
Thermus sp. [TaxId: 275]
(2)
2a
d1gkpa2
A:55-389
2b
d1gkpb2
B:55-389
2c
d1gkpc2
C:55-389
2d
d1gkpd2
D:55-389
2e
d1gkpe2
E:55-389
2f
d1gkpf2
F:55-389
[
close SCOP info
]
CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_1gkpB02 (B:54-382)
1b: CATH_1gkpA02 (A:54-383,A:399-423)
1c: CATH_1gkpC02 (C:54-383,C:399-423)
1d: CATH_1gkpD02 (D:54-383,D:399-423)
1e: CATH_1gkpE02 (E:54-383,E:399-423)
1f: CATH_1gkpF02 (F:54-383,F:399-423)
2a: CATH_1gkpB01 (B:2-53,B:383-459)
2b: CATH_1gkpA01 (A:2-53,A:389-396,A:424-444)
2c: CATH_1gkpC01 (C:2-53,C:389-396,C:424-444)
2d: CATH_1gkpD01 (D:2-53,D:389-396,D:424-444)
2e: CATH_1gkpE01 (E:2-53,E:389-396,E:424-444)
2f: CATH_1gkpF01 (F:2-53,F:389-396,F:424-444)
View:
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)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Metal-dependent hydrolases
(190)
Thermus sp.. Organism_taxid: 275.
(2)
1a
1gkpB02
B:54-382
1b
1gkpA02
A:54-383,A:399-423
1c
1gkpC02
C:54-383,C:399-423
1d
1gkpD02
D:54-383,D:399-423
1e
1gkpE02
E:54-383,E:399-423
1f
1gkpF02
F:54-383,F:399-423
Class
:
Mainly Beta
(13760)
Architecture
:
Roll
(1513)
Topology
:
Urease, subunit C; domain 1
(95)
Homologous Superfamily
:
Urease, subunit C, domain 1
(95)
Thermus sp.. Organism_taxid: 275.
(2)
2a
1gkpB01
B:2-53,B:383-459
2b
1gkpA01
A:2-53,A:389-396,A:424-444
2c
1gkpC01
C:2-53,C:389-396,C:424-444
2d
1gkpD01
D:2-53,D:389-396,D:424-444
2e
1gkpE01
E:2-53,E:389-396,E:424-444
2f
1gkpF01
F:2-53,F:389-396,F:424-444
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Asym.Unit (1.0 MB)
Header - Asym.Unit
Biol.Unit 1 (677 KB)
Header - Biol.Unit 1
Biol.Unit 2 (681 KB)
Header - Biol.Unit 2
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