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1GKF
Asym. Unit
Info
Asym.Unit (153 KB)
Biol.Unit 1 (147 KB)
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(1)
Title
:
CRYSTAL STRUCTURES OF PENICILLIN ACYLASE ENZYME-SUBSTRATE COMPLEXES: STRUCTURAL INSIGHTS INTO THE CATALYTIC MECHANISM
Authors
:
C. E. Mcvey, M. A. Walsh, G. G. Dodson, K. S. Wilson, J. A. Brannigan
Date
:
13 Aug 01 (Deposition) - 04 Jan 02 (Release) - 07 Dec 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.41
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Antibiotic Resistance, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. E. Mcvey, M. A. Walsh, G. G. Dodson, K. S. Wilson, J. A. Brannigan
Crystal Structures Of Penicillin Acylase Enzyme- Substrate Complexes: Structural Insights Into The Catalytic Mechanism
J. Mol. Biol. V. 313 139 2001
(for further references see the
PDB file header
)
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Hetero Components
(3, 15)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
3a: METHIONINE SULFOXIDE (SMEa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
1
Ligand/Ion
CALCIUM ION
2
EDO
13
Ligand/Ion
1,2-ETHANEDIOL
3
SME
1
Mod. Amino Acid
METHIONINE SULFOXIDE
[
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Sites
(14, 14)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:152 , ASP B:73 , VAL B:75 , ASP B:76 , PRO B:205 , ASP B:252
BINDING SITE FOR RESIDUE CA B1571
02
AC2
SOFTWARE
ALA B:241 , PHE B:256 , LEU B:257 , ASN B:388 , LYS B:394 , HOH B:2324 , HOH B:2645
BINDING SITE FOR RESIDUE EDO B1558
03
AC3
SOFTWARE
LEU A:156 , THR A:208 , ALA B:79 , TYR B:137 , PRO B:208 , PRO B:210 , HOH B:2274 , HOH B:2646 , HOH B:2647
BINDING SITE FOR RESIDUE EDO B1559
04
AC4
SOFTWARE
GLN B:288 , ARG B:291 , ILE B:329 , EDO B:1561 , HOH B:2648
BINDING SITE FOR RESIDUE EDO B1560
05
AC5
SOFTWARE
ASP B:327 , ILE B:329 , EDO B:1560 , HOH B:2649
BINDING SITE FOR RESIDUE EDO B1561
06
AC6
SOFTWARE
ALA B:171 , GLN B:173 , GLY B:194 , ALA B:195 , PHE B:223 , ASN B:226 , HOH B:2239 , HOH B:2245 , HOH B:2286 , HOH B:2650
BINDING SITE FOR RESIDUE EDO B1562
07
AC7
SOFTWARE
HOH A:2206 , SER B:234 , TYR B:236 , HOH B:2651 , HOH B:2652 , HOH B:2654
BINDING SITE FOR RESIDUE EDO B1563
08
AC8
SOFTWARE
PRO A:187 , THR A:188 , TYR B:236 , ALA B:238 , ASP B:268 , HOH B:2652 , HOH B:2654
BINDING SITE FOR RESIDUE EDO B1564
09
AC9
SOFTWARE
GLN A:37 , ASP A:38 , SER B:508 , ASP B:518 , HOH B:2655
BINDING SITE FOR RESIDUE EDO B1565
10
BC1
SOFTWARE
GLU B:475 , GLU B:529 , ASN B:530 , HOH B:2608
BINDING SITE FOR RESIDUE EDO B1566
11
BC2
SOFTWARE
THR A:125 , GLN B:273 , LYS B:274 , HOH B:2656 , HOH B:2657
BINDING SITE FOR RESIDUE EDO B1567
12
BC3
SOFTWARE
TYR A:197 , MET B:225 , ASN B:226 , PRO B:227 , LYS B:228 , GLN B:245 , HOH B:2658
BINDING SITE FOR RESIDUE EDO B1568
13
BC4
SOFTWARE
TYR A:197 , PHE A:201 , ASP B:73 , ARG B:199 , LEU B:221 , PRO B:249 , HOH B:2313 , HOH B:2659
BINDING SITE FOR RESIDUE EDO B1569
14
BC5
SOFTWARE
GLY B:375 , LEU B:387 , ASN B:388 , SER B:390 , HOH B:2660
BINDING SITE FOR RESIDUE EDO B1570
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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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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.
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1gkf_1 (A:,B:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ntn hydrolase-like
(356)
Superfamily
:
N-terminal nucleophile aminohydrolases (Ntn hydrolases)
(352)
Family
:
Penicillin acylase, catalytic domain
(37)
Protein domain
:
Penicillin acylase
(25)
Escherichia coli [TaxId: 562]
(24)
1a
d1gkf.1
A:,B:
[
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]
CATH Domains
(5, 5)
Info
all CATH domains
1a: CATH_1gkfB01 (B:1-72,B:146-290,B:452-536)
2a: CATH_1gkfA02 (A:150-179)
3a: CATH_1gkfB03 (B:291-451)
4a: CATH_1gkfA01 (A:3-149)
5a: CATH_1gkfB02 (B:73-145)
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)
(
)
Architectures
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)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
4-Layer Sandwich
(459)
Topology
:
Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
(128)
Homologous Superfamily
:
Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
(124)
Escherichia coli. Organism_taxid: 562.
(21)
1a
1gkfB01
B:1-72,B:146-290,B:452-536
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
[code=1.10.287.150, no name defined]
(24)
Escherichia coli. Organism_taxid: 562.
(18)
2a
1gkfA02
A:150-179
Topology
:
Penicillin amidase (Acylase) alpha subunit, N-terminal domain
(46)
Homologous Superfamily
:
[code=1.10.1400.10, no name defined]
(46)
Escherichia coli. Organism_taxid: 562.
(18)
3a
1gkfB03
B:291-451
Topology
:
Penicillin Amidohydrolase; domain 1
(47)
Homologous Superfamily
:
Penicillin Amidohydrolase, domain 1
(47)
Escherichia coli. Organism_taxid: 562.
(18)
4a
1gkfA01
A:3-149
Class
:
Mainly Beta
(13760)
Architecture
:
Roll
(1513)
Topology
:
Penicillin G acylase, beta-roll domain
(38)
Homologous Superfamily
:
[code=2.30.120.10, no name defined]
(38)
Escherichia coli. Organism_taxid: 562.
(18)
5a
1gkfB02
B:73-145
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Atom Selection
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Protein
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Protein & NOT Site
Protein & NOT PROSITE
Chain A
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Asymmetric Unit 1
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select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
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View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
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Asym.Unit (153 KB)
Header - Asym.Unit
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Header - Biol.Unit 1
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