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3DC2
Biol. Unit 1
Info
Asym.Unit (166 KB)
Biol.Unit 1 (312 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF SERINE BOUND D-3-PHOSPHOGLYCERATE DEHYDROGENASE FROM MYCOBACTERIUM TUBERCULOSIS
Authors
:
S. Dey, J. C. Sacchettini
Date
:
03 Jun 08 (Deposition) - 22 Jul 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Oxidoreductase, Phosphoglycerate Dehydrogenase, Serine Biosynthesis, Amino-Acid Biosynthesis, Nad
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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)
Reference
:
S. Dey, R. L. Burton, G. A. Grant, J. C. Sacchettini
Structural Analysis Of Substrate And Effector Binding In Mycobacterium Tuberculosis D-3-Phosphoglycerate Dehydrogenase
Biochemistry V. 47 8271 2008
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Hetero Components
(2, 10)
Info
All Hetero Components
1a: SERINE (SERa)
1b: SERINE (SERb)
2a: L(+)-TARTARIC ACID (TLAa)
2b: L(+)-TARTARIC ACID (TLAb)
2c: L(+)-TARTARIC ACID (TLAc)
View:
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Label:
No.
Name
Count
Type
Full Name
1
SER
4
Mod. Amino Acid
SERINE
2
TLA
6
Ligand/Ion
L(+)-TARTARIC ACID
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Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TYR A:461 , ASP A:463 , ARG A:464 , PRO A:465 , GLY A:466 , ALA A:467 , LEU A:468 , LEU A:487 , ASN B:481 , ILE B:482
BINDING SITE FOR RESIDUE SER A 600
2
AC2
SOFTWARE
ASN A:481 , ILE A:482 , TYR B:461 , ASP B:463 , ARG B:464 , GLY B:466 , LEU B:468 , LEU B:487
BINDING SITE FOR RESIDUE SER B 600
3
AC3
SOFTWARE
ARG A:446 , HIS A:447 , HOH A:817 , LYS B:439 , ASP B:449 , LEU B:450 , ARG B:451 , ARG B:501
BINDING SITE FOR RESIDUE TLA A 700
4
AC4
SOFTWARE
LYS A:439 , ASP A:449 , LEU A:450 , ARG A:451 , ALA A:484 , ARG A:501 , ARG B:446 , HIS B:447 , SER B:488
BINDING SITE FOR RESIDUE TLA B 700
5
AC5
SOFTWARE
GLU B:361 , GLU B:363 , LYS B:402
BINDING SITE FOR RESIDUE TLA B 701
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(4, 32)
Info
All PROSITE Patterns/Profiles
1: D_2_HYDROXYACID_DH_1 (A:145-172,B:145-172)
2: D_2_HYDROXYACID_DH_2 (A:193-215,B:193-215)
3: D_2_HYDROXYACID_DH_3 (A:222-238,B:222-238)
4: ACT (A:456-528,B:456-528)
;
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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_MYCTO
144-171
4
A:145-172
B:145-172
SERA_MYCTU
144-171
4
A:145-172
B:145-172
2
D_2_HYDROXYACID_DH_2
PS00670
D-isomer specific 2-hydroxyacid dehydrogenases signature 2.
SERA_MYCTO
192-214
4
A:193-215
B:193-215
SERA_MYCTU
192-214
4
A:193-215
B:193-215
3
D_2_HYDROXYACID_DH_3
PS00671
D-isomer specific 2-hydroxyacid dehydrogenases signature 3.
SERA_MYCTO
221-237
4
A:222-238
B:222-238
SERA_MYCTU
221-237
4
A:222-238
B:222-238
4
ACT
PS51671
ACT domain profile.
SERA_MYCTO
455-527
4
A:456-528
B:456-528
SERA_MYCTU
455-527
4
A:456-528
B:456-528
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Exons
(0, 0)
Info
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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
(4, 8)
Info
All SCOP Domains
1a: SCOP_d3dc2a4 (A:452-529)
1b: SCOP_d3dc2b4 (B:452-529)
2a: SCOP_d3dc2a3 (A:317-451)
2b: SCOP_d3dc2b3 (B:317-451)
3a: SCOP_d3dc2a1 (A:4-98,A:283-316)
3b: SCOP_d3dc2b1 (B:4-98,B:283-316)
4a: SCOP_d3dc2a2 (A:99-282)
4b: SCOP_d3dc2b2 (B:99-282)
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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)
Mycobacterium tuberculosis [TaxId: 1773]
(2)
1a
d3dc2a4
A:452-529
1b
d3dc2b4
B:452-529
Fold
:
FwdE/GAPDH domain-like
(188)
Superfamily
:
Serine metabolism enzymes domain
(5)
Family
:
SerA intervening domain-like
(2)
Protein domain
:
D-3-phosphoglycerate dehydrogenase SerA
(2)
Mycobacterium tuberculosis [TaxId: 1773]
(2)
2a
d3dc2a3
A:317-451
2b
d3dc2b3
B:317-451
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)
Mycobacterium tuberculosis [TaxId: 1773]
(2)
3a
d3dc2a1
A:4-98,A:283-316
3b
d3dc2b1
B:4-98,B:283-316
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)
Mycobacterium tuberculosis [TaxId: 1773]
(2)
4a
d3dc2a2
A:99-282
4b
d3dc2b2
B:99-282
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CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_3dc2B03 (B:316-454)
1b: CATH_3dc2A03 (A:321-453)
2a: CATH_3dc2A02 (A:99-280)
2b: CATH_3dc2B02 (B:100-280)
2c: CATH_3dc2A01 (A:4-98,A:281-320)
2d: CATH_3dc2B01 (B:4-99,B:281-315)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
60s Ribosomal Protein L30; Chain: A;
(235)
Homologous Superfamily
:
D-3-phosphoglycerate dehydrogenase; domain 3
(5)
Mycobacterium tuberculosis. Organism_taxid: 1773. Strain: h37rv.
(2)
1a
3dc2B03
B:316-454
1b
3dc2A03
A:321-453
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Mycobacterium tuberculosis. Organism_taxid: 1773. Strain: h37rv.
(2)
2a
3dc2A02
A:99-280
2b
3dc2B02
B:100-280
2c
3dc2A01
A:4-98,A:281-320
2d
3dc2B01
B:4-99,B:281-315
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Pfam Domains
(0, 0)
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