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2P9E
Asym. Unit
Info
Asym.Unit (264 KB)
Biol.Unit 1 (256 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF G336V MUTANT OF E.COLI PHOSPHOGLYCERATE DEHYDROGENASE
Authors
:
S. Dey, J. C. Sacchettini
Date
:
25 Mar 07 (Deposition) - 24 Apr 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Oxidoreductase, G336V Mutant, Phosphoglycerate Dehydrogenase, Serine Biosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Dey, Z. Hu, X. L. Xu, J. C. Sacchettini, G. A. Grant
The Effect Of Hinge Mutations On Effector Binding And Domain Rotation In Escherichia Coli D-3-Phosphoglycerate Dehydrogenase
J. Biol. Chem. V. 282 18418 2007
(for further references see the
PDB file header
)
[
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Hetero Components
(4, 19)
Info
All Hetero Components
1a: CITRIC ACID (CITa)
1b: CITRIC ACID (CITb)
1c: CITRIC ACID (CITc)
1d: CITRIC ACID (CITd)
1e: CITRIC ACID (CITe)
1f: CITRIC ACID (CITf)
2a: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIa)
2b: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIb)
2c: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIc)
2d: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAId)
3a: PHOSPHATE ION (PO4a)
3b: PHOSPHATE ION (PO4b)
3c: PHOSPHATE ION (PO4c)
3d: PHOSPHATE ION (PO4d)
3e: PHOSPHATE ION (PO4e)
3f: PHOSPHATE ION (PO4f)
3g: PHOSPHATE ION (PO4g)
3h: PHOSPHATE ION (PO4h)
4a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CIT
6
Ligand/Ion
CITRIC ACID
2
NAI
4
Ligand/Ion
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
3
PO4
8
Ligand/Ion
PHOSPHATE ION
4
SO4
1
Ligand/Ion
SULFATE ION
[
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Sites
(19, 19)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS B:196 , LEU B:197 , SER B:198
BINDING SITE FOR RESIDUE PO4 B 499
02
AC2
SOFTWARE
LEU A:142 , ALA A:143 , ALA A:144 , ARG B:60
BINDING SITE FOR RESIDUE PO4 A 500
03
AC3
SOFTWARE
ARG C:60 , HOH C:589 , LEU D:142 , ALA D:143 , ALA D:144
BINDING SITE FOR RESIDUE PO4 C 501
04
AC4
SOFTWARE
LEU C:142 , ALA C:143 , ALA C:144 , ARG D:60
BINDING SITE FOR RESIDUE PO4 C 502
05
AC5
SOFTWARE
ARG A:60 , LEU B:142 , ALA B:143 , ALA B:144
BINDING SITE FOR RESIDUE PO4 B 503
06
AC6
SOFTWARE
GLY A:85 , THR A:86 , ASN A:87 , ARG A:240
BINDING SITE FOR RESIDUE PO4 A 504
07
AC7
SOFTWARE
ARG D:60 , SER D:61 , ALA D:83
BINDING SITE FOR RESIDUE PO4 D 505
08
AC8
SOFTWARE
HIS C:38 , LYS C:39 , GLY C:40
BINDING SITE FOR RESIDUE SO4 C 506
09
AC9
SOFTWARE
HIS D:38 , LYS D:39 , GLY D:40
BINDING SITE FOR RESIDUE PO4 D 507
10
BC1
SOFTWARE
ILE A:84 , PHE A:106 , GLY A:158 , GLY A:160 , HIS A:161 , ILE A:162 , TYR A:180 , ASP A:181 , ILE A:182 , LYS A:185 , HIS A:210 , VAL A:211 , PRO A:212 , SER A:216 , THR A:217 , MET A:220 , ALA A:238 , SER A:239 , ARG A:240 , ASP A:264 , VAL A:265 , HIS A:292 , GLY A:294 , GLY A:295
BINDING SITE FOR RESIDUE NAI A 508
11
BC2
SOFTWARE
ILE B:84 , PHE B:106 , ASN B:108 , VAL B:112 , TYR B:159 , GLY B:160 , HIS B:161 , ILE B:162 , ASP B:181 , ILE B:182 , HIS B:210 , VAL B:211 , PRO B:212 , SER B:216 , MET B:220 , ALA B:238 , SER B:239 , ARG B:240 , ASP B:264 , HIS B:292 , GLY B:294 , GLY B:295
BINDING SITE FOR RESIDUE NAI B 509
12
BC3
SOFTWARE
ILE C:84 , PHE C:106 , ASN C:108 , VAL C:112 , GLY C:158 , GLY C:160 , HIS C:161 , ILE C:162 , ASP C:181 , ILE C:182 , HIS C:210 , VAL C:211 , PRO C:212 , SER C:216 , ALA C:238 , SER C:239 , ARG C:240 , ASP C:264 , HIS C:292 , GLY C:294 , GLY C:295
BINDING SITE FOR RESIDUE NAI C 510
13
BC4
SOFTWARE
ASN D:108 , VAL D:112 , GLY D:158 , TYR D:159 , GLY D:160 , HIS D:161 , ILE D:162 , TYR D:180 , ASP D:181 , ILE D:182 , LYS D:185 , HIS D:210 , VAL D:211 , PRO D:212 , SER D:216 , ALA D:238 , SER D:239 , ARG D:240 , ASP D:264 , VAL D:265 , HIS D:292 , GLY D:294 , GLY D:295 , HOH D:558
BINDING SITE FOR RESIDUE NAI D 511
14
BC5
SOFTWARE
LYS B:39 , TYR D:180 , HIS D:196 , LEU D:197 , SER D:198 , GLU D:225
BINDING SITE FOR RESIDUE CIT D 513
15
BC6
SOFTWARE
TYR A:180 , HIS A:196 , LEU A:197 , SER A:198
BINDING SITE FOR RESIDUE CIT A 514
16
BC7
SOFTWARE
TYR C:180 , HIS C:196 , LEU C:197 , SER C:198
BINDING SITE FOR RESIDUE CIT C 515
17
BC8
SOFTWARE
LYS A:141 , ARG B:60 , SER B:61 , ALA B:83 , ILE B:84 , GLY B:85 , ASN B:108
BINDING SITE FOR RESIDUE CIT B 516
18
BC9
SOFTWARE
ARG C:60 , SER C:61 , ALA C:83 , ILE C:84 , ASN C:108 , HOH C:553 , LYS D:141
BINDING SITE FOR RESIDUE CIT C 517
19
CC1
SOFTWARE
PHE A:37 , HIS A:38 , LYS A:39 , GLY A:40 , ALA A:41 , LEU A:42
BINDING SITE FOR RESIDUE CIT A 518
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(4, 16)
Info
All PROSITE Patterns/Profiles
1: D_2_HYDROXYACID_DH_1 (A:154-181,B:154-181,C:154-181,D:15...)
2: D_2_HYDROXYACID_DH_2 (A:200-222,B:200-222,C:200-222,D:20...)
3: D_2_HYDROXYACID_DH_3 (A:229-245,B:229-245,C:229-245,D:22...)
4: ACT (A:339-410,B:339-410,C:339-410,D:33...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
D_2_HYDROXYACID_DH_1
PS00065
D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature.
SERA_ECOLI
154-181
4
A:154-181
B:154-181
C:154-181
D:154-181
2
D_2_HYDROXYACID_DH_2
PS00670
D-isomer specific 2-hydroxyacid dehydrogenases signature 2.
SERA_ECOLI
200-222
4
A:200-222
B:200-222
C:200-222
D:200-222
3
D_2_HYDROXYACID_DH_3
PS00671
D-isomer specific 2-hydroxyacid dehydrogenases signature 3.
SERA_ECOLI
229-245
4
A:229-245
B:229-245
C:229-245
D:229-245
4
ACT
PS51671
ACT domain profile.
SERA_ECOLI
339-410
4
A:339-410
B:339-410
C:339-410
D:339-410
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(3, 12)
Info
All SCOP Domains
1a: SCOP_d2p9ea3 (A:327-410)
1b: SCOP_d2p9eb3 (B:327-410)
1c: SCOP_d2p9ec3 (C:327-410)
1d: SCOP_d2p9ed3 (D:327-410)
2a: SCOP_d2p9ea2 (A:7-107,A:296-326)
2b: SCOP_d2p9eb2 (B:7-107,B:296-326)
2c: SCOP_d2p9ec2 (C:7-107,C:296-326)
2d: SCOP_d2p9ed2 (D:8-107,D:296-326)
3a: SCOP_d2p9ea1 (A:108-295)
3b: SCOP_d2p9eb1 (B:108-295)
3c: SCOP_d2p9ec1 (C:108-295)
3d: SCOP_d2p9ed1 (D:108-295)
View:
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Classes
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)
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)
Folds
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(
)
Superfamilies
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)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
ACT-like
(63)
Family
:
Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain
(9)
Protein domain
:
Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain
(9)
Escherichia coli [TaxId: 562]
(7)
1a
d2p9ea3
A:327-410
1b
d2p9eb3
B:327-410
1c
d2p9ec3
C:327-410
1d
d2p9ed3
D:327-410
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Flavodoxin-like
(1057)
Superfamily
:
Formate/glycerate dehydrogenase catalytic domain-like
(49)
Family
:
Formate/glycerate dehydrogenases, substrate-binding domain
(21)
Protein domain
:
Phosphoglycerate dehydrogenase
(9)
Escherichia coli [TaxId: 562]
(7)
2a
d2p9ea2
A:7-107,A:296-326
2b
d2p9eb2
B:7-107,B:296-326
2c
d2p9ec2
C:7-107,C:296-326
2d
d2p9ed2
D:8-107,D:296-326
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Formate/glycerate dehydrogenases, NAD-domain
(49)
Protein domain
:
Phosphoglycerate dehydrogenase
(9)
Escherichia coli [TaxId: 562]
(7)
3a
d2p9ea1
A:108-295
3b
d2p9eb1
B:108-295
3c
d2p9ec1
C:108-295
3d
d2p9ed1
D:108-295
[
close SCOP info
]
CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_2p9eA03 (A:328-409)
1b: CATH_2p9eB03 (B:328-409)
1c: CATH_2p9eC03 (C:328-409)
1d: CATH_2p9eD03 (D:328-409)
2a: CATH_2p9eA02 (A:109-297)
2b: CATH_2p9eA01 (A:5-108,A:298-326)
2c: CATH_2p9eC01 (C:5-108,C:298-326)
2d: CATH_2p9eB01 (B:7-108,B:298-326)
2e: CATH_2p9eD01 (D:8-108,D:298-326)
2f: CATH_2p9eB02 (B:109-297)
2g: CATH_2p9eC02 (C:109-297)
2h: CATH_2p9eD02 (D:109-297)
View:
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Classes
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)
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)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.260, no name defined]
(34)
Escherichia coli. Organism_taxid: 562.
(7)
1a
2p9eA03
A:328-409
1b
2p9eB03
B:328-409
1c
2p9eC03
C:328-409
1d
2p9eD03
D:328-409
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Escherichia coli. Organism_taxid: 562.
(48)
2a
2p9eA02
A:109-297
2b
2p9eA01
A:5-108,A:298-326
2c
2p9eC01
C:5-108,C:298-326
2d
2p9eB01
B:7-108,B:298-326
2e
2p9eD01
D:8-108,D:298-326
2f
2p9eB02
B:109-297
2g
2p9eC02
C:109-297
2h
2p9eD02
D:109-297
[
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]
Pfam Domains
(3, 12)
Info
all PFAM domains
1a: PFAM_ACT_2p9eD01 (D:339-402)
1b: PFAM_ACT_2p9eD02 (D:339-402)
1c: PFAM_ACT_2p9eD03 (D:339-402)
1d: PFAM_ACT_2p9eD04 (D:339-402)
2a: PFAM_2_Hacid_dh_2p9eD05 (D:13-326)
2b: PFAM_2_Hacid_dh_2p9eD06 (D:13-326)
2c: PFAM_2_Hacid_dh_2p9eD07 (D:13-326)
2d: PFAM_2_Hacid_dh_2p9eD08 (D:13-326)
3a: PFAM_2_Hacid_dh_C_2p9eD09 (D:117-294)
3b: PFAM_2_Hacid_dh_C_2p9eD10 (D:117-294)
3c: PFAM_2_Hacid_dh_C_2p9eD11 (D:117-294)
3d: PFAM_2_Hacid_dh_C_2p9eD12 (D:117-294)
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Clans
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Organisms
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)
Clan
:
ACT
(34)
Family
:
ACT
(19)
Escherichia coli (strain K12)
(5)
1a
ACT-2p9eD01
D:339-402
1b
ACT-2p9eD02
D:339-402
1c
ACT-2p9eD03
D:339-402
1d
ACT-2p9eD04
D:339-402
Clan
:
Form_Glyc_dh
(56)
Family
:
2-Hacid_dh
(21)
Escherichia coli (strain K12)
(5)
2a
2-Hacid_dh-2p9eD05
D:13-326
2b
2-Hacid_dh-2p9eD06
D:13-326
2c
2-Hacid_dh-2p9eD07
D:13-326
2d
2-Hacid_dh-2p9eD08
D:13-326
Clan
:
NADP_Rossmann
(1239)
Family
:
2-Hacid_dh_C
(23)
Escherichia coli (strain K12)
(5)
3a
2-Hacid_dh_C-2p9eD09
D:117-294
3b
2-Hacid_dh_C-2p9eD10
D:117-294
3c
2-Hacid_dh_C-2p9eD11
D:117-294
3d
2-Hacid_dh_C-2p9eD12
D:117-294
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