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Biol.Unit 1 (60 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE OF WILD TYPE PENICILLIN-BINDING PROTEIN 5 FROM E. COLI
Authors
:
R. A. Nicholas, S. Krings, J. Tomberg, G. Nicola, C. Davies
Date
:
19 Feb 03 (Deposition) - 13 Jan 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.85
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Peptidoglycan Synthesis, Penicillin-Binding Protein, Dd- Carboxypeptidase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. A. Nicholas, S. Krings, J. Tomberg, G. Nicola, C. Davies
Crystal Structure Of Wild-Type Penicillin-Binding Protein 5 From Escherichia Coli: Implications For Deacylation Of The Acyl-Enzyme Complex.
J. Biol. Chem. V. 278 52826 2003
(for further references see the
PDB file header
)
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: BETA-MERCAPTOETHANOL (BMEa)
1b: BETA-MERCAPTOETHANOL (BMEb)
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No.
Name
Count
Type
Full Name
1
BME
2
Ligand/Ion
BETA-MERCAPTOETHANOL
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LEU A:308 , ALA A:310
BINDING SITE FOR RESIDUE BME A 364
2
AC2
SOFTWARE
TYR A:25 , ASN A:26 , GLN A:232 , ARG A:234
BINDING SITE FOR RESIDUE BME A 365
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SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_DACA_ECOLI_001 (G105D, chain A, )
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dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_DACA_ECOLI_001
*
G
134
D
DACA_ECOLI
---
---
A
G
105
D
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(0, 0)
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Exons
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d1nzoa1 (A:263-355)
2a: SCOP_d1nzoa2 (A:4-262)
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Protein Domains
(
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(
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(
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(
)
Class
:
All beta proteins
(24004)
Fold
:
Penicillin-binding protein associated domain
(19)
Superfamily
:
Penicillin-binding protein associated domain
(19)
Family
:
PBP5 C-terminal domain-like
(12)
Protein domain
:
Penicillin-binding protein 5, C-terminal domain
(11)
Escherichia coli [TaxId: 562]
(11)
1a
d1nzoa1
A:263-355
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
beta-lactamase/transpeptidase-like
(515)
Superfamily
:
beta-lactamase/transpeptidase-like
(515)
Family
:
beta-Lactamase/D-ala carboxypeptidase
(411)
Protein domain
:
Penicillin-binding protein 5, N-terminal domain
(11)
Escherichia coli [TaxId: 562]
(11)
2a
d1nzoa2
A:4-262
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CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_1nzoA01 (A:4-262)
2a: CATH_1nzoA02 (A:263-354)
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)
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Beta-lactamase
(339)
Homologous Superfamily
:
DD-peptidase/beta-lactamase superfamily
(335)
Escherichia coli. Organism_taxid: 562.
(91)
1a
1nzoA01
A:4-262
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Peptidoglycan synthesis regulatory factor (PBP3), Domain 2
(13)
Homologous Superfamily
:
Peptidoglycan synthesis regulatory factor (PBP3), Domain 2
(13)
Escherichia coli. Organism_taxid: 562.
(9)
2a
1nzoA02
A:263-354
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Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_Peptidase_S11_1nzoA01 (A:6-244)
2a: PFAM_PBP5_C_1nzoA02 (A:263-354)
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Clan
:
Beta-lactamase
(210)
Family
:
Peptidase_S11
(12)
Escherichia coli (strain K12)
(6)
1a
Peptidase_S11-1nzoA01
A:6-244
Clan
:
no clan defined [family: PBP5_C]
(10)
Family
:
PBP5_C
(10)
Escherichia coli (strain K12)
(6)
2a
PBP5_C-1nzoA02
A:263-354
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