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2P9G
Biol. Unit 1
Info
Asym.Unit (133 KB)
Biol.Unit 1 (253 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF SERINE BOUND G336V,G337V DOUBLE MUTANT OF E.COLI PHOSPHOGLYCERATE DEHYDROGENASE
Authors
:
S. Dey, J. C. Sacchettini
Date
:
25 Mar 07 (Deposition) - 24 Apr 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Oxidoreductase, Serine Biosynthesis, D-3-Phosphoglycerate Dehydrogenase, Double Mutation
(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 Domai Rotation In Escherichia Coli D-3-Phosphoglycerate Dehydrogenase.
J. Biol. Chem. V. 282 18418 2007
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIa)
1b: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIb)
2a: SERINE (SERa)
2b: SERINE (SERb)
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Label:
No.
Name
Count
Type
Full Name
1
NAI
4
Ligand/Ion
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
2
SER
4
Mod. Amino Acid
SERINE
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ILE A:84 , PHE A:106 , TYR A:159 , 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 , ALA A:238 , SER A:239 , ARG A:240 , ASP A:264 , HIS A:292 , GLY A:294 , GLY A:295
BINDING SITE FOR RESIDUE NAI A 450
2
AC2
SOFTWARE
PHE B:106 , ASN B:108 , GLY B:160 , HIS B:161 , ILE B:162 , ASP B:181 , ILE B:182 , LYS B:185 , HIS B:210 , VAL B:211 , PRO B:212 , SER B:216 , THR B:217 , MET B:220 , ALA B:238 , SER B:239 , ARG B:240 , ASP B:264 , HIS B:292 , GLY B:295
BINDING SITE FOR RESIDUE NAI B 550
3
AC3
SOFTWARE
HIS A:344 , ASN A:346 , ARG A:347 , GLY A:349 , VAL A:350 , LEU A:351 , LEU A:370 , HOH A:546 , ASN B:364 , ILE B:365
BINDING SITE FOR RESIDUE SER A 451
4
AC4
SOFTWARE
ASN A:364 , ILE A:365 , HOH A:517 , HIS B:344 , ASN B:346 , ARG B:347 , PRO B:348 , GLY B:349 , VAL B:350 , LEU B:370 , THR B:372
BINDING SITE FOR RESIDUE SER A 551
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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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)
2: D_2_HYDROXYACID_DH_2 (A:200-222,B:200-222)
3: D_2_HYDROXYACID_DH_3 (A:229-245,B:229-245)
4: ACT (A:339-410,B:339-410)
;
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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
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
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
4
ACT
PS51671
ACT domain profile.
SERA_ECOLI
339-410
4
A:339-410
B:339-410
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Exons
(0, 0)
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d2p9ga3 (A:327-410)
1b: SCOP_d2p9gb3 (B:327-410)
2a: SCOP_d2p9ga2 (A:7-107,A:296-326)
2b: SCOP_d2p9gb2 (B:7-107,B:296-326)
3a: SCOP_d2p9ga1 (A:108-295)
3b: SCOP_d2p9gb1 (B:108-295)
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)
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)
(
)
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
d2p9ga3
A:327-410
1b
d2p9gb3
B: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
d2p9ga2
A:7-107,A:296-326
2b
d2p9gb2
B:7-107,B: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
d2p9ga1
A:108-295
3b
d2p9gb1
B:108-295
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CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_2p9gA03 (A:328-409)
1b: CATH_2p9gB03 (B:328-409)
2a: CATH_2p9gA02 (A:109-297)
2b: CATH_2p9gA01 (A:7-108,A:298-326)
2c: CATH_2p9gB01 (B:7-108,B:298-326)
2d: CATH_2p9gB02 (B:109-297)
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)
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)
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
2p9gA03
A:328-409
1b
2p9gB03
B: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
2p9gA02
A:109-297
2b
2p9gA01
A:7-108,A:298-326
2c
2p9gB01
B:7-108,B:298-326
2d
2p9gB02
B:109-297
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Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_ACT_2p9gB01 (B:339-402)
1b: PFAM_ACT_2p9gB02 (B:339-402)
2a: PFAM_2_Hacid_dh_2p9gB03 (B:13-326)
2b: PFAM_2_Hacid_dh_2p9gB04 (B:13-326)
3a: PFAM_2_Hacid_dh_C_2p9gB05 (B:117-294)
3b: PFAM_2_Hacid_dh_C_2p9gB06 (B:117-294)
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)
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(
)
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)
Clan
:
ACT
(34)
Family
:
ACT
(19)
Escherichia coli (strain K12)
(5)
1a
ACT-2p9gB01
B:339-402
1b
ACT-2p9gB02
B:339-402
Clan
:
Form_Glyc_dh
(56)
Family
:
2-Hacid_dh
(21)
Escherichia coli (strain K12)
(5)
2a
2-Hacid_dh-2p9gB03
B:13-326
2b
2-Hacid_dh-2p9gB04
B:13-326
Clan
:
NADP_Rossmann
(1239)
Family
:
2-Hacid_dh_C
(23)
Escherichia coli (strain K12)
(5)
3a
2-Hacid_dh_C-2p9gB05
B:117-294
3b
2-Hacid_dh_C-2p9gB06
B:117-294
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