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1SC6
Asym. Unit
Info
Asym.Unit (260 KB)
Biol.Unit 1 (250 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF W139G D-3-PHOSPHOGLYCERATE DEHYDROGENASE COMPLEXED WITH NAD+
Authors
:
J. K. Bell, G. A. Grant, L. J. Banaszak
Date
:
11 Feb 04 (Deposition) - 22 Feb 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.09
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Allosteric Regulation Phosphoglycerate Dehydrogenase Pgdh, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. K. Bell, G. A. Grant, L. J. Banaszak
Multiconformational States In Phosphoglycerate Dehydrogenase
Biochemistry V. 43 3450 2004
(for further references see the
PDB file header
)
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Hetero Components
(2, 36)
Info
All Hetero Components
1a: SELENOMETHIONINE (MSEa)
1aa: SELENOMETHIONINE (MSEaa)
1ab: SELENOMETHIONINE (MSEab)
1ac: SELENOMETHIONINE (MSEac)
1ad: SELENOMETHIONINE (MSEad)
1ae: SELENOMETHIONINE (MSEae)
1af: SELENOMETHIONINE (MSEaf)
1b: SELENOMETHIONINE (MSEb)
1c: SELENOMETHIONINE (MSEc)
1d: SELENOMETHIONINE (MSEd)
1e: SELENOMETHIONINE (MSEe)
1f: SELENOMETHIONINE (MSEf)
1g: SELENOMETHIONINE (MSEg)
1h: SELENOMETHIONINE (MSEh)
1i: SELENOMETHIONINE (MSEi)
1j: SELENOMETHIONINE (MSEj)
1k: SELENOMETHIONINE (MSEk)
1l: SELENOMETHIONINE (MSEl)
1m: SELENOMETHIONINE (MSEm)
1n: SELENOMETHIONINE (MSEn)
1o: SELENOMETHIONINE (MSEo)
1p: SELENOMETHIONINE (MSEp)
1q: SELENOMETHIONINE (MSEq)
1r: SELENOMETHIONINE (MSEr)
1s: SELENOMETHIONINE (MSEs)
1t: SELENOMETHIONINE (MSEt)
1u: SELENOMETHIONINE (MSEu)
1v: SELENOMETHIONINE (MSEv)
1w: SELENOMETHIONINE (MSEw)
1x: SELENOMETHIONINE (MSEx)
1y: SELENOMETHIONINE (MSEy)
1z: SELENOMETHIONINE (MSEz)
2a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
2b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
2c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
2d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MSE
32
Mod. Amino Acid
SELENOMETHIONINE
2
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
PRO A:105 , PHE A:106 , ASN A:108 , THR A:109 , GLY A:158 , TYR A:159 , GLY A:160 , HIS A:161 , ILE A:162 , ASP A:181 , ILE A:182 , LYS A:185 , HIS A:210 , VAL A:211 , PRO A:212 , SER A:216 , THR A:217 , ARG A:240 , HOH A:1616 , HOH A:1894
BINDING SITE FOR RESIDUE NAD A 2101
2
AC2
SOFTWARE
ILE B:84 , PRO B:105 , PHE B:106 , ASN B:108 , THR B:109 , GLY B:158 , TYR B:159 , 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 , SER B:239 , HOH B:1601 , HOH B:1671 , HOH B:1717 , HOH B:1871 , HOH B:1893 , HOH B:1958
BINDING SITE FOR RESIDUE NAD B 2102
3
AC3
SOFTWARE
PRO C:105 , PHE C:106 , ASN C:108 , THR C:109 , GLY C:158 , TYR C:159 , GLY C:160 , HIS C:161 , ILE C:162 , ASP C:181 , ILE C:182 , LYS C:185 , HIS C:210 , VAL C:211 , PRO C:212 , SER C:216 , THR C:217 , HOH C:1611 , HOH C:1637 , HOH C:1869 , HOH C:1900 , HOH C:1942
BINDING SITE FOR RESIDUE NAD C 2103
4
AC4
SOFTWARE
PRO D:105 , PHE D:106 , ASN D:108 , THR D:109 , 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 , THR D:217 , SER D:239 , HOH D:1600 , HOH D:1732 , HOH D:1943
BINDING SITE FOR RESIDUE NAD D 2104
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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
(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:
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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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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_d1sc6a3 (A:327-410)
1b: SCOP_d1sc6b3 (B:327-410)
1c: SCOP_d1sc6c3 (C:327-410)
1d: SCOP_d1sc6d3 (D:327-410)
2a: SCOP_d1sc6a2 (A:7-107,A:296-326)
2b: SCOP_d1sc6b2 (B:7-107,B:296-326)
2c: SCOP_d1sc6c2 (C:9-107,C:299-326)
2d: SCOP_d1sc6d2 (D:7-107,D:296-326)
3a: SCOP_d1sc6a1 (A:108-295)
3b: SCOP_d1sc6b1 (B:108-295)
3c: SCOP_d1sc6c1 (C:108-291)
3d: SCOP_d1sc6d1 (D:108-291)
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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
d1sc6a3
A:327-410
1b
d1sc6b3
B:327-410
1c
d1sc6c3
C:327-410
1d
d1sc6d3
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
d1sc6a2
A:7-107,A:296-326
2b
d1sc6b2
B:7-107,B:296-326
2c
d1sc6c2
C:9-107,C:299-326
2d
d1sc6d2
D:7-107,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
d1sc6a1
A:108-295
3b
d1sc6b1
B:108-295
3c
d1sc6c1
C:108-291
3d
d1sc6d1
D:108-291
[
close SCOP info
]
CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_1sc6A03 (A:328-409)
1b: CATH_1sc6B03 (B:328-409)
1c: CATH_1sc6C03 (C:328-409)
1d: CATH_1sc6D03 (D:328-409)
2a: CATH_1sc6A02 (A:109-295)
2b: CATH_1sc6D02 (D:109-297)
2c: CATH_1sc6B02 (B:109-295)
2d: CATH_1sc6C02 (C:109-291)
2e: CATH_1sc6A01 (A:7-108,A:296-326)
2f: CATH_1sc6B01 (B:7-108,B:296-326)
2g: CATH_1sc6D01 (D:7-108,D:298-326)
2h: CATH_1sc6C01 (C:9-108,C:299-326)
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)
(
)
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
1sc6A03
A:328-409
1b
1sc6B03
B:328-409
1c
1sc6C03
C:328-409
1d
1sc6D03
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
1sc6A02
A:109-295
2b
1sc6D02
D:109-297
2c
1sc6B02
B:109-295
2d
1sc6C02
C:109-291
2e
1sc6A01
A:7-108,A:296-326
2f
1sc6B01
B:7-108,B:296-326
2g
1sc6D01
D:7-108,D:298-326
2h
1sc6C01
C:9-108,C:299-326
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Asym.Unit (260 KB)
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