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4UBP
Asym. Unit
Info
Asym.Unit (145 KB)
Biol.Unit 1 (138 KB)
Biol.Unit 2 (406 KB)
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(1)
Title
:
STRUCTURE OF BACILLUS PASTEURII UREASE INHIBITED WITH ACETOHYDROXAMIC ACID AT 1.55 A RESOLUTION
Authors
:
S. Benini, W. R. Rypniewski, K. S. Wilson, S. Ciurli, S. Mangani
Date
:
25 Feb 99 (Deposition) - 06 Mar 00 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.55
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: A,B,C (3x)
Keywords
:
Urease, Bacillus Pasteurii, Nickel, Acetohydroxamic Acid, Metalloenzyme, Hydrolase
(Keyword Search:
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Reference
:
S. Benini, W. R. Rypniewski, K. S. Wilson, S. Miletti, S. Ciurli, S. Mangani
The Complex Of Bacillus Pasteurii Urease With Acetohydroxamate Anion From X-Ray Data At 1. 55 A Resolution
J. Biol. Inorg. Chem. V. 5 110 2000
(for further references see the
PDB file header
)
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Hetero Components
(4, 5)
Info
All Hetero Components
1a: ACETYL GROUP (ACEa)
2a: ACETOHYDROXAMIC ACID (HAEa)
3a: LYSINE NZ-CARBOXYLIC ACID (KCXa)
4a: NICKEL (II) ION (NIa)
4b: NICKEL (II) ION (NIb)
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No.
Name
Count
Type
Full Name
1
ACE
1
Mod. Amino Acid
ACETYL GROUP
2
HAE
1
Ligand/Ion
ACETOHYDROXAMIC ACID
3
KCX
1
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
4
NI
2
Ligand/Ion
NICKEL (II) ION
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: CAT (AUTHOR)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
KCX C:220 , HIS C:222 , HIS C:249 , HIS C:275 , GLY C:280 , NI C:799 , HAE C:800
BINDING SITE FOR RESIDUE NI C 798
2
AC2
SOFTWARE
HIS C:137 , HIS C:139 , KCX C:220 , ASP C:363 , NI C:798 , HAE C:800
BINDING SITE FOR RESIDUE NI C 799
3
AC3
SOFTWARE
HIS C:137 , ALA C:170 , KCX C:220 , HIS C:222 , HIS C:249 , HIS C:275 , GLY C:280 , ASP C:363 , NI C:798 , NI C:799
BINDING SITE FOR RESIDUE HAE C 800
4
CAT
AUTHOR
HIS C:137 , HIS C:139 , KCX C:220 , HIS C:249 , HIS C:275 , ASP C:363
THE DINUCLEAR NI2+ METALLOCENTER IS INHIBITED BY A MOLECULE OF ACETOHYDROXAMIC ACID
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
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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
(4, 4)
Info
All SCOP Domains
1a: SCOP_d4ubpb_ (B:)
2a: SCOP_d4ubpc1 (C:1-131,C:435-483)
3a: SCOP_d4ubpa_ (A:)
4a: SCOP_d4ubpc2 (C:132-434,C:484-570)
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Protein Domains
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)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
beta-clip
(280)
Superfamily
:
Urease, beta-subunit
(40)
Family
:
Urease, beta-subunit
(40)
Protein domain
:
Urease, beta-subunit
(39)
Bacillus pasteurii [TaxId: 1474]
(6)
1a
d4ubpb_
B:
Fold
:
Composite domain of metallo-dependent hydrolases
(103)
Superfamily
:
Composite domain of metallo-dependent hydrolases
(103)
Family
:
alpha-Subunit of urease
(40)
Protein domain
:
alpha-Subunit of urease
(40)
Bacillus pasteurii [TaxId: 1474]
(7)
2a
d4ubpc1
C:1-131,C:435-483
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Urease, gamma-subunit
(42)
Superfamily
:
Urease, gamma-subunit
(42)
Family
:
Urease, gamma-subunit
(40)
Protein domain
:
Urease, gamma-subunit
(40)
Bacillus pasteurii [TaxId: 1474]
(7)
3a
d4ubpa_
A:
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Metallo-dependent hydrolases
(273)
Family
:
alpha-subunit of urease, catalytic domain
(40)
Protein domain
:
alpha-subunit of urease, catalytic domain
(40)
Bacillus pasteurii [TaxId: 1474]
(7)
4a
d4ubpc2
C:132-434,C:484-570
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CATH Domains
(4, 4)
Info
all CATH domains
1a: CATH_4ubpA00 (A:1-100)
2a: CATH_4ubpC02 (C:132-425,C:484-569)
3a: CATH_4ubpB00 (B:5-126)
4a: CATH_4ubpC01 (C:1-131,C:426-483)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Urease; subunit A
(36)
Homologous Superfamily
:
Urease, subunit A
(36)
Sporosarcina pasteurii. Organism_taxid: 1474. Strain: dsm 33.
(3)
1a
4ubpA00
A:1-100
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Metal-dependent hydrolases
(190)
Sporosarcina pasteurii. Organism_taxid: 1474. Strain: dsm 33.
(3)
2a
4ubpC02
C:132-425,C:484-569
Class
:
Mainly Beta
(13760)
Architecture
:
Ribbon
(789)
Topology
:
Urease, subunit B
(35)
Homologous Superfamily
:
Urease, subunit B
(35)
Sporosarcina pasteurii. Organism_taxid: 1474. Strain: dsm 33.
(3)
3a
4ubpB00
B:5-126
Architecture
:
Roll
(1513)
Topology
:
Urease, subunit C; domain 1
(95)
Homologous Superfamily
:
Urease, subunit C, domain 1
(95)
Sporosarcina pasteurii. Organism_taxid: 1474. Strain: dsm 33.
(3)
4a
4ubpC01
C:1-131,C:426-483
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Asymmetric Unit 1
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Asym.Unit (145 KB)
Header - Asym.Unit
Biol.Unit 1 (138 KB)
Header - Biol.Unit 1
Biol.Unit 2 (406 KB)
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