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2ZM8
Asym. Unit
Info
Asym.Unit (77 KB)
Biol.Unit 1 (142 KB)
Biol.Unit 2 (72 KB)
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(1)
Title
:
STRUCTURE OF 6-AMINOHEXANOATE-DIMER HYDROLASE, S112A/D370Y MUTANT COMPLEXED WITH 6-AMINOHEXANOATE-DIMER
Authors
:
T. Ohki, N. Shibata, Y. Higuchi, Y. Kawashima, M. Takeo, D. Kato, S. Nego
Date
:
14 Apr 08 (Deposition) - 14 Apr 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.55
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Biol. Unit 2: A (1x)
Keywords
:
Alpha-Beta, Hydrolase, Nylon Degradation
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Ohki, N. Shibata, Y. Higuchi, Y. Kawashima, M. Takeo, D. Kato, S. Negoro
Two Alternative Modes For Optimizing Nylon-6 Byproduct Hydrolytic Activity From A Carboxylesterase With A Beta-Lactamase Fold: X-Ray Crystallographic Analysis Of Directly Evolved 6-Aminohexanoate-Dimer Hydrolase.
Protein Sci. V. 18 1662 2009
[
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Hetero Components
(4, 11)
Info
All Hetero Components
1a: 6-AMINOHEXANOIC ACID (ACAa)
1b: 6-AMINOHEXANOIC ACID (ACAb)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
3a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
3b: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESb)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACA
2
Ligand/Ion
6-AMINOHEXANOIC ACID
2
GOL
5
Ligand/Ion
GLYCEROL
3
MES
2
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4
SO4
2
Ligand/Ion
SULFATE ION
[
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Sites
(22, 22)
Info
All Sites
01: AC1 (unknown)
02: AC2 (unknown)
03: AC3 (unknown)
04: AC4 (unknown)
05: AC5 (unknown)
06: AC6 (unknown)
07: AC7 (unknown)
08: AC8 (unknown)
09: AC9 (unknown)
10: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
19: AE1 (SOFTWARE)
20: AE2 (SOFTWARE)
21: BC1 (unknown)
22: BC2 (unknown)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
unknown
ARG A:205 , HOH A:920
BINDING SITE FOR RESIDUE SO4 A 509
02
AC2
unknown
ARG A:107 , ARG A:251 , ASP A:252 , HOH A:779 , HOH A:796
BINDING SITE FOR RESIDUE SO4 A 510
03
AC3
unknown
ALA A:112 , TYR A:170 , TYR A:215 , PHE A:317 , TRP A:331 , ILE A:345 , TYR A:370 , HIS A:375 , HOH A:812
BINDING SITE FOR RESIDUE ACA A 511
04
AC4
unknown
MET A:111 , ALA A:112 , TYR A:170 , TRP A:186 , HIS A:266 , GLY A:344 , ILE A:345 , HOH A:909 , HOH A:956
BINDING SITE FOR RESIDUE ACA A 512
05
AC5
unknown
TYR A:13 , PRO A:30 , TRP A:34 , HIS A:38 , ARG A:99 , GLY A:101 , HIS A:309 , GLU A:310 , HOH A:577 , HOH A:725 , HOH A:751 , HOH A:820 , HOH A:892
BINDING SITE FOR RESIDUE MES A 502
06
AC6
unknown
LEU A:70 , PRO A:71 , ASP A:72 , ARG A:76 , HOH A:760
BINDING SITE FOR RESIDUE MES A 503
07
AC7
unknown
GLN A:79 , GLY A:211 , GLU A:310 , ALA A:311 , HOH A:620 , HOH A:891
BINDING SITE FOR RESIDUE GOL A 504
08
AC8
unknown
ALA A:37 , ASP A:106 , ARG A:107 , ARG A:251 , HOH A:661 , HOH A:704 , HOH A:733 , HOH A:766
BINDING SITE FOR RESIDUE GOL A 505
09
AC9
unknown
ASP A:24 , GLN A:27 , GLU A:28 , PRO A:173 , ARG A:187 , HOH A:566 , HOH A:883 , HOH A:899 , HOH A:934
BINDING SITE FOR RESIDUE GOL A 506
10
AD1
SOFTWARE
ARG A:205 , HOH A:920
BINDING SITE FOR RESIDUE SO4 A 509
11
AD2
SOFTWARE
ARG A:107 , ARG A:251 , ASP A:252 , HOH A:779 , HOH A:796
BINDING SITE FOR RESIDUE SO4 A 510
12
AD3
SOFTWARE
ALA A:112 , TYR A:170 , TYR A:215 , PHE A:317 , TRP A:331 , ILE A:345 , TYR A:370 , HIS A:375 , ACA A:512 , HOH A:812
BINDING SITE FOR RESIDUE ACA A 511
13
AD4
SOFTWARE
MET A:111 , ALA A:112 , TYR A:170 , TRP A:186 , HIS A:266 , GLY A:344 , ILE A:345 , ACA A:511 , HOH A:909 , HOH A:956
BINDING SITE FOR RESIDUE ACA A 512
14
AD5
SOFTWARE
TYR A:13 , PRO A:30 , TRP A:34 , HIS A:38 , ARG A:99 , GLY A:101 , HIS A:309 , GLU A:310 , HOH A:577 , HOH A:725 , HOH A:751 , HOH A:820 , HOH A:892
BINDING SITE FOR RESIDUE MES A 502
15
AD6
SOFTWARE
LEU A:70 , PRO A:71 , ASP A:72 , ARG A:76 , HOH A:760
BINDING SITE FOR RESIDUE MES A 503
16
AD7
SOFTWARE
GLN A:79 , GLY A:211 , GLU A:310 , ALA A:311 , HOH A:620 , HOH A:891
BINDING SITE FOR RESIDUE GOL A 504
17
AD8
SOFTWARE
ALA A:37 , ASP A:106 , ARG A:107 , ARG A:251 , HOH A:661 , HOH A:704 , HOH A:733 , HOH A:766
BINDING SITE FOR RESIDUE GOL A 505
18
AD9
SOFTWARE
ASP A:24 , GLN A:27 , GLU A:28 , VAL A:171 , PRO A:173 , ARG A:187 , HOH A:566 , HOH A:883 , HOH A:899 , HOH A:934
BINDING SITE FOR RESIDUE GOL A 506
19
AE1
SOFTWARE
THR A:91 , ARG A:274 , HOH A:594
BINDING SITE FOR RESIDUE GOL A 507
20
AE2
SOFTWARE
ASP A:159 , GLN A:161 , GLY A:306 , GLY A:307 , SER A:308 , THR A:327 , ARG A:328 , HOH A:726 , HOH A:980
BINDING SITE FOR RESIDUE GOL A 508
21
BC1
unknown
THR A:91 , ARG A:274 , HOH A:594
BINDING SITE FOR RESIDUE GOL A 507
22
BC2
unknown
ASP A:159 , GLN A:161 , GLY A:306 , GLY A:307 , SER A:308 , THR A:327 , ARG A:328 , HOH A:726 , HOH A:980
BINDING SITE FOR RESIDUE GOL A 508
[
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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
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;
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Sorry, no Info available
[
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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_d2zm8a_ (A:)
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Classes
(
)
(
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Folds
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Superfamilies
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
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
:
6-aminohexanoate-dimer hydrolase NylC
(11)
Flavobacterium sp. [TaxId: 239]
(11)
1a
d2zm8a_
A:
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Beta_lactamase_2zm8A01 (A:72-378)
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Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Beta-lactamase
(210)
Family
:
Beta-lactamase
(79)
Flavobacterium sp. (strain K172)
(8)
1a
Beta-lactamase-2zm8A01
A:72-378
[
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Atom Selection
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All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
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select residue range 5 to 10 in chain 'A'
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Show PDB file:
Asym.Unit (77 KB)
Header - Asym.Unit
Biol.Unit 1 (142 KB)
Header - Biol.Unit 1
Biol.Unit 2 (72 KB)
Header - Biol.Unit 2
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