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Asym. Unit
Info
Asym.Unit (214 KB)
Biol.Unit 1 (208 KB)
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(1)
Title
:
STRUCTURE OF THE E192N MUTANT OF E. COLI N-ACETYLNEURAMINIC ACID LYASE IN COMPLEX WITH PYRUVATE IN CRYSTAL FORM III
Authors
:
I. Campeotto, G. N. Murshudov, A. H. Bolt, C. H. Trinh, S. E. V. Phillips, A. R. Pearson, A. Berry
Date
:
28 May 10 (Deposition) - 22 Sep 10 (Release) - 13 Mar 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.65
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
I. Campeotto, A. H. Bolt, T. A. Harman, C. Dennis, C. H. Trinh, S. E. V. Phillips, A. Nelson, A. R. Pearson, A. Berry
Structural Insights Into Substrate Specificity In Variants Of N-Acetylneuraminic Acid Lyase Produced By Directed Evolution.
To Be Published
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Hetero Components
(3, 14)
Info
All Hetero Components
1a: PENTAETHYLENE GLYCOL (1PEa)
1b: PENTAETHYLENE GLYCOL (1PEb)
1c: PENTAETHYLENE GLYCOL (1PEc)
1d: PENTAETHYLENE GLYCOL (1PEd)
2a: (2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-P... (KPIa)
2b: (2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-P... (KPIb)
2c: (2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-P... (KPIc)
2d: (2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-P... (KPId)
3a: PYRUVIC ACID (PYRa)
3b: PYRUVIC ACID (PYRb)
3c: PYRUVIC ACID (PYRc)
3d: PYRUVIC ACID (PYRd)
3e: PYRUVIC ACID (PYRe)
3f: PYRUVIC ACID (PYRf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PE
4
Ligand/Ion
PENTAETHYLENE GLYCOL
2
KPI
4
Mod. Amino Acid
(2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-PROPAN-2-YLIDENE)AMINO]HEXANOIC ACID
3
PYR
6
Ligand/Ion
PYRUVIC ACID
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Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR B:190 , ASP B:191 , ASN B:192 , HOH B:2172
BINDING SITE FOR RESIDUE PYR B1297
02
AC2
SOFTWARE
TYR A:190 , ASP A:191 , ASN A:192 , SER A:208 , HOH A:2256
BINDING SITE FOR RESIDUE PYR A1298
03
AC3
SOFTWARE
GLY D:189 , TYR D:190 , ASP D:191 , ASN D:192 , SER D:208 , HOH D:2256 , HOH D:2257
BINDING SITE FOR RESIDUE PYR D1298
04
AC4
SOFTWARE
TYR C:190 , ASP C:191 , ASN C:192 , HOH C:2173 , HOH C:2175
BINDING SITE FOR RESIDUE PYR C1298
05
AC5
SOFTWARE
LEU B:142 , HOH B:2107 , ALA C:141 , GLY C:144 , HOH C:2116
BINDING SITE FOR RESIDUE PYR C1299
06
AC6
SOFTWARE
LYS C:234 , LEU C:235 , GLU C:238 , GLU C:295
BINDING SITE FOR RESIDUE PYR C1300
07
AC7
SOFTWARE
ASP A:263
BINDING SITE FOR RESIDUE 1PE A1299
08
AC8
SOFTWARE
GLN D:37 , GLU D:295
BINDING SITE FOR RESIDUE 1PE D1299
09
AC9
SOFTWARE
LYS A:73 , LYS A:75 , ASP A:101
BINDING SITE FOR RESIDUE 1PE A1300
10
BC1
SOFTWARE
PRO A:140 , ALA A:141 , GLY A:144 , PRO D:140 , ALA D:141 , GLY D:144
BINDING SITE FOR RESIDUE 1PE D1300
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: DHDPS_1 (A:41-58,B:41-58,C:41-58,D:41-58,A:...)
2: DHDPS_2 (A:137-167,B:137-167,C:137-167,D:13...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DHDPS_1
PS00665
Dihydrodipicolinate synthase signature 1.
NANA_ECO8A
41-58
4
A:41-58
B:41-58
C:41-58
D:41-58
NANA_ECOLI
41-58
4
A:41-58
B:41-58
C:41-58
D:41-58
2
DHDPS_2
PS00666
Dihydrodipicolinate synthase signature 2.
NANA_ECO8A
137-167
4
A:137-167
B:137-167
C:137-167
D:137-167
NANA_ECOLI
137-167
4
A:137-167
B:137-167
C:137-167
D:137-167
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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, 4)
Info
All SCOP Domains
1a: SCOP_d2xfwa_ (A:)
1b: SCOP_d2xfwb_ (B:)
1c: SCOP_d2xfwc_ (C:)
1d: SCOP_d2xfwd_ (D:)
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)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Aldolase
(457)
Family
:
Class I aldolase
(182)
Protein domain
:
automated matches
(54)
Escherichia coli [TaxId: 469008]
(5)
1a
d2xfwa_
A:
1b
d2xfwb_
B:
1c
d2xfwc_
C:
1d
d2xfwd_
D:
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2xfwB00 (B:-1-296)
1b: CATH_2xfwA00 (A:-1-297)
1c: CATH_2xfwC00 (C:-1-297)
1d: CATH_2xfwD00 (D:-1-297)
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(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Aldolase class I
(887)
Escherichia coli. Organism_taxid: 562.
(44)
1a
2xfwB00
B:-1-296
1b
2xfwA00
A:-1-297
1c
2xfwC00
C:-1-297
1d
2xfwD00
D:-1-297
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_DHDPS_2xfwD01 (D:4-293)
1b: PFAM_DHDPS_2xfwD02 (D:4-293)
1c: PFAM_DHDPS_2xfwD03 (D:4-293)
1d: PFAM_DHDPS_2xfwD04 (D:4-293)
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Clan
:
TIM_barrel
(694)
Family
:
DHDPS
(40)
Escherichia coli O8 (strain IAI1)
(1)
1a
DHDPS-2xfwD01
D:4-293
1b
DHDPS-2xfwD02
D:4-293
1c
DHDPS-2xfwD03
D:4-293
1d
DHDPS-2xfwD04
D:4-293
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Asymmetric Unit 1
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select residue range 5 to 10 in chain 'A'
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