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1GK9
Asym. Unit
Info
Asym.Unit (159 KB)
Biol.Unit 1 (152 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
:
10 Aug 01 (Deposition) - 04 Jan 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Antibiotic Resistance, Amidase, Ntn-Hydrolase,
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. E. Mcvey, M. A. Walsh, G. G. Dodson, K. S, 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
(2, 25)
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)
2n: 1,2-ETHANEDIOL (EDOn)
2o: 1,2-ETHANEDIOL (EDOo)
2p: 1,2-ETHANEDIOL (EDOp)
2q: 1,2-ETHANEDIOL (EDOq)
2r: 1,2-ETHANEDIOL (EDOr)
2s: 1,2-ETHANEDIOL (EDOs)
2t: 1,2-ETHANEDIOL (EDOt)
2u: 1,2-ETHANEDIOL (EDOu)
2v: 1,2-ETHANEDIOL (EDOv)
2w: 1,2-ETHANEDIOL (EDOw)
2x: 1,2-ETHANEDIOL (EDOx)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
1
Ligand/Ion
CALCIUM ION
2
EDO
24
Ligand/Ion
1,2-ETHANEDIOL
[
close Hetero Component info
]
Sites
(25, 25)
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)
24: CC6 (SOFTWARE)
25: CC7 (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 B1579
02
AC2
SOFTWARE
THR A:150 , SER A:151 , GLU A:152 , ILE A:153 , ASP A:154 , ILE B:77
BINDING SITE FOR RESIDUE EDO A1210
03
AC3
SOFTWARE
LEU A:181 , VAL A:182 , LYS A:200 , PHE A:201 , GLN A:203 , HOH A:2253
BINDING SITE FOR RESIDUE EDO A1211
04
AC4
SOFTWARE
LEU A:156 , THR A:160 , LYS A:163 , ASN A:205 , HOH A:2254
BINDING SITE FOR RESIDUE EDO A1212
05
AC5
SOFTWARE
SER B:234 , TYR B:236 , EDO B:1574 , HOH B:2647 , HOH B:2648 , HOH B:2649 , HOH B:2662
BINDING SITE FOR RESIDUE EDO B1558
06
AC6
SOFTWARE
PHE B:256 , LEU B:257 , ASN B:388 , LYS B:394 , HOH B:2449 , HOH B:2650
BINDING SITE FOR RESIDUE EDO B1559
07
AC7
SOFTWARE
PHE A:146 , SER B:1 , GLN B:23 , ALA B:69 , ASN B:241 , EDO B:1562 , EDO B:1564 , HOH B:2446
BINDING SITE FOR RESIDUE EDO B1560
08
AC8
SOFTWARE
ASP B:293 , LEU B:294 , ASN B:295 , GLY B:375 , TYR B:376 , ASN B:388 , HOH B:2651
BINDING SITE FOR RESIDUE EDO B1561
09
AC9
SOFTWARE
SER B:1 , PHE B:24 , SER B:67 , THR B:68 , ALA B:69 , EDO B:1560
BINDING SITE FOR RESIDUE EDO B1562
10
BC1
SOFTWARE
TYR A:197 , PHE A:201 , ASP B:73 , ARG B:199 , LEU B:221 , HOH B:2248 , HOH B:2301
BINDING SITE FOR RESIDUE EDO B1563
11
BC2
SOFTWARE
ARG B:263 , SER B:386 , ASN B:388 , EDO B:1560 , HOH B:2446 , HOH B:2652 , HOH B:2653
BINDING SITE FOR RESIDUE EDO B1564
12
BC3
SOFTWARE
ALA B:79 , PRO B:208 , PRO B:210 , HOH B:2655
BINDING SITE FOR RESIDUE EDO B1565
13
BC4
SOFTWARE
LYS A:179 , LEU A:181 , ASP B:73 , PRO B:205 , ARG B:206 , ALA B:250 , SER B:251 , ASP B:252 , HOH B:2656
BINDING SITE FOR RESIDUE EDO B1566
14
BC5
SOFTWARE
ASN B:185 , ASN B:187 , HOH B:2397 , HOH B:2657
BINDING SITE FOR RESIDUE EDO B1567
15
BC6
SOFTWARE
ASP B:327 , ILE B:329 , EDO B:1571 , EDO B:1578
BINDING SITE FOR RESIDUE EDO B1568
16
BC7
SOFTWARE
GLN A:37 , ASP A:38 , SER B:508 , ASP B:518 , HOH B:2658
BINDING SITE FOR RESIDUE EDO B1569
17
BC8
SOFTWARE
PHE A:201 , ASN A:202 , GLN B:200 , SER B:201 , GLY B:202 , HIS B:203
BINDING SITE FOR RESIDUE EDO B1570
18
BC9
SOFTWARE
GLN B:288 , ARG B:291 , ILE B:329 , EDO B:1568 , HOH B:2659
BINDING SITE FOR RESIDUE EDO B1571
19
CC1
SOFTWARE
GLY B:375 , SER B:386 , LEU B:387 , ASN B:388 , HOH B:2653 , HOH B:2660
BINDING SITE FOR RESIDUE EDO B1572
20
CC2
SOFTWARE
ARG B:291 , GLU B:475 , GLN B:477 , GLU B:529 , ASN B:530 , HOH B:2600 , HOH B:2661
BINDING SITE FOR RESIDUE EDO B1573
21
CC3
SOFTWARE
PRO A:187 , THR A:188 , ALA B:238 , VAL B:264 , ASP B:268 , EDO B:1558 , HOH B:2662
BINDING SITE FOR RESIDUE EDO B1574
22
CC4
SOFTWARE
ASN A:196 , TYR A:197 , PRO A:198 , GLU B:224 , MET B:225 , ASN B:226 , PRO B:227 , LYS B:228 , GLN B:245 , HOH B:2664 , HOH B:2665
BINDING SITE FOR RESIDUE EDO B1575
23
CC5
SOFTWARE
ARG B:269 , ARG B:297 , PRO B:301 , HOH B:2666
BINDING SITE FOR RESIDUE EDO B1576
24
CC6
SOFTWARE
LYS B:10 , GLU B:272 , PRO B:275 , HOH B:2667 , HOH B:2668
BINDING SITE FOR RESIDUE EDO B1577
25
CC7
SOFTWARE
ARG B:325 , TRP B:326 , ASP B:327 , EDO B:1568 , HOH B:2669
BINDING SITE FOR RESIDUE EDO B1578
[
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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
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1gk9_1 (A:,B:)
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Classes
(
)
(
)
Folds
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(
)
Superfamilies
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)
(
)
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
d1gk9.1
A:,B:
[
close SCOP info
]
CATH Domains
(5, 5)
Info
all CATH domains
1a: CATH_1gk9B01 (B:1-72,B:146-290,B:452-536)
2a: CATH_1gk9A02 (A:150-179)
3a: CATH_1gk9B03 (B:291-451)
4a: CATH_1gk9A01 (A:2-149)
5a: CATH_1gk9B02 (B:73-145)
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Homologous Superfamilies
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)
(
)
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
1gk9B01
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
1gk9A02
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
1gk9B03
B:291-451
Topology
:
Penicillin Amidohydrolase; domain 1
(47)
Homologous Superfamily
:
Penicillin Amidohydrolase, domain 1
(47)
Escherichia coli. Organism_taxid: 562.
(18)
4a
1gk9A01
A:2-149
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
1gk9B02
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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