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2X0N
Biol. Unit 1
Info
Asym.Unit (694 KB)
Biol.Unit 1 (456 KB)
Biol.Unit 2 (459 KB)
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(1)
Title
:
STRUCTURE OF GLYCOSOMAL GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM TRYPANOSOMA BRUCEI DETERMINED FROM LAUE DATA
Authors
:
F. M. D. Vellieux, J. Hajdu, W. G. J. Hol
Date
:
16 Dec 09 (Deposition) - 22 Dec 09 (Release) - 25 Jan 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.20
Chains
:
Asym. Unit : A,B,O,P,Q,R
Biol. Unit 1: A,B (2x)
Biol. Unit 2: O,P,Q,R (1x)
Keywords
:
Glycolysis, Glycosome, Oxidoreductase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
F. M. D. Vellieux, J. Hajdu, C. L. Verlinde, H. Groendijk, R. J. Read, T. J. Greenhough, J. W. Campbell, K. H. Kalk, J. A. Littlechild, H. C. Watson
Structure Of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase From Trypanosoma Brucei Determined From Laue Data.
Proc. Natl. Acad. Sci. Usa V. 90 2355 1993
(for further references see the
PDB file header
)
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Hetero Components
(2, 12)
Info
All Hetero Components
1a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
1b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
1c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
1d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
1e: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADe)
1f: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADf)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
2i: SULFATE ION (SO4i)
2j: SULFATE ION (SO4j)
2k: SULFATE ION (SO4k)
2l: SULFATE ION (SO4l)
View:
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Label:
No.
Name
Count
Type
Full Name
1
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2
SO4
8
Ligand/Ion
SULFATE ION
[
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
THR A:196 , THR A:198 , NAD A:361
BINDING SITE FOR RESIDUE SO4 A 359
2
AC2
SOFTWARE
SER A:164 , THR A:225 , GLY A:226 , ALA A:227
BINDING SITE FOR RESIDUE SO4 A 360
3
AC3
SOFTWARE
GLY A:8 , GLY A:10 , ARG A:11 , ILE A:12 , ASP A:37 , MET A:38 , ALA A:89 , GLN A:90 , SER A:109 , THR A:110 , GLY A:111 , LEU A:112 , SER A:133 , ALA A:134 , CYS A:165 , ALA A:197 , ASN A:334 , SO4 A:359
BINDING SITE FOR RESIDUE NAD A 361
4
AC4
SOFTWARE
THR B:196 , THR B:198 , ARG B:248
BINDING SITE FOR RESIDUE SO4 B 359
5
AC5
SOFTWARE
SER B:164 , THR B:225 , GLY B:226 , ALA B:227
BINDING SITE FOR RESIDUE SO4 B 360
6
AC6
SOFTWARE
ASN B:7 , GLY B:8 , GLY B:10 , ARG B:11 , ILE B:12 , ASP B:37 , MET B:38 , ALA B:89 , GLN B:90 , SER B:109 , THR B:110 , GLY B:111 , LEU B:112 , SER B:133 , ALA B:134 , ALA B:197 , ASN B:334
BINDING SITE FOR RESIDUE NAD B 361
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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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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: GAPDH (A:163-170,B:163-170)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GAPDH
PS00071
Glyceraldehyde 3-phosphate dehydrogenase active site.
G3PG_TRYBB
164-171
4
A:163-170
B:163-170
-
-
-
-
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
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
(2, 12)
Info
All SCOP Domains
1a: SCOP_d2x0na2 (A:165-333)
1b: SCOP_d2x0nb2 (B:165-333)
1c: SCOP_d2x0no2 (O:165-333)
1d: SCOP_d2x0np2 (P:165-333)
1e: SCOP_d2x0nq2 (Q:165-333)
1f: SCOP_d2x0nr2 (R:165-333)
2a: SCOP_d2x0na1 (A:1-164,A:334-358)
2b: SCOP_d2x0nb1 (B:1-164,B:334-358)
2c: SCOP_d2x0no1 (O:1-164,O:334-358)
2d: SCOP_d2x0np1 (P:1-164,P:334-358)
2e: SCOP_d2x0nq1 (Q:1-164,Q:334-358)
2f: SCOP_d2x0nr1 (R:1-164,R:334-358)
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Classes
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)
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)
Folds
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)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
FwdE/GAPDH domain-like
(188)
Superfamily
:
Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
(179)
Family
:
GAPDH-like
(99)
Protein domain
:
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)
(61)
Trypanosoma brucei brucei, glycosome [TaxId: 5702]
(1)
1a
d2x0na2
A:165-333
1b
d2x0nb2
B:165-333
1c
d2x0no2
O:165-333
1d
d2x0np2
P:165-333
1e
d2x0nq2
Q:165-333
1f
d2x0nr2
R:165-333
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
(179)
Protein domain
:
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)
(61)
Trypanosoma brucei brucei, glycosome [TaxId: 5702]
(1)
2a
d2x0na1
A:1-164,A:334-358
2b
d2x0nb1
B:1-164,B:334-358
2c
d2x0no1
O:1-164,O:334-358
2d
d2x0np1
P:1-164,P:334-358
2e
d2x0nq1
Q:1-164,Q:334-358
2f
d2x0nr1
R:1-164,R:334-358
[
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]
CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_2x0nA02 (A:164-334)
1b: CATH_2x0nB02 (B:164-334)
1c: CATH_2x0nO02 (O:164-334)
1d: CATH_2x0nP02 (P:164-334)
1e: CATH_2x0nQ02 (Q:164-334)
1f: CATH_2x0nR02 (R:164-334)
2a: CATH_2x0nA01 (A:1-163,A:335-354)
2b: CATH_2x0nB01 (B:1-163,B:335-354)
2c: CATH_2x0nO01 (O:1-163,O:335-354)
2d: CATH_2x0nP01 (P:1-163,P:335-354)
2e: CATH_2x0nQ01 (Q:1-163,Q:335-354)
2f: CATH_2x0nR01 (R:1-163,R:335-354)
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Dihydrodipicolinate Reductase; domain 2
(182)
Homologous Superfamily
:
Dihydrodipicolinate Reductase; domain 2
(178)
Trypanosoma brucei brucei. Organism_taxid: 5702
(1)
1a
2x0nA02
A:164-334
1b
2x0nB02
B:164-334
1c
2x0nO02
O:164-334
1d
2x0nP02
P:164-334
1e
2x0nQ02
Q:164-334
1f
2x0nR02
R:164-334
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Trypanosoma brucei brucei. Organism_taxid: 5702
(1)
2a
2x0nA01
A:1-163,A:335-354
2b
2x0nB01
B:1-163,B:335-354
2c
2x0nO01
O:1-163,O:335-354
2d
2x0nP01
P:1-163,P:335-354
2e
2x0nQ01
Q:1-163,Q:335-354
2f
2x0nR01
R:1-163,R:335-354
[
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Pfam Domains
(2, 12)
Info
all PFAM domains
1a: PFAM_Gp_dh_C_2x0nR01 (R:170-332)
1b: PFAM_Gp_dh_C_2x0nR02 (R:170-332)
1c: PFAM_Gp_dh_C_2x0nR03 (R:170-332)
1d: PFAM_Gp_dh_C_2x0nR04 (R:170-332)
1e: PFAM_Gp_dh_C_2x0nR05 (R:170-332)
1f: PFAM_Gp_dh_C_2x0nR06 (R:170-332)
2a: PFAM_Gp_dh_N_2x0nR07 (R:2-165)
2b: PFAM_Gp_dh_N_2x0nR08 (R:2-165)
2c: PFAM_Gp_dh_N_2x0nR09 (R:2-165)
2d: PFAM_Gp_dh_N_2x0nR10 (R:2-165)
2e: PFAM_Gp_dh_N_2x0nR11 (R:2-165)
2f: PFAM_Gp_dh_N_2x0nR12 (R:2-165)
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)
Organisms
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)
Clan
:
GADPH_aa-bio_dh
(59)
Family
:
Gp_dh_C
(38)
Trypanosoma brucei brucei
(1)
1a
Gp_dh_C-2x0nR01
R:170-332
1b
Gp_dh_C-2x0nR02
R:170-332
1c
Gp_dh_C-2x0nR03
R:170-332
1d
Gp_dh_C-2x0nR04
R:170-332
1e
Gp_dh_C-2x0nR05
R:170-332
1f
Gp_dh_C-2x0nR06
R:170-332
Clan
:
NADP_Rossmann
(1239)
Family
:
Gp_dh_N
(38)
Trypanosoma brucei brucei
(1)
2a
Gp_dh_N-2x0nR07
R:2-165
2b
Gp_dh_N-2x0nR08
R:2-165
2c
Gp_dh_N-2x0nR09
R:2-165
2d
Gp_dh_N-2x0nR10
R:2-165
2e
Gp_dh_N-2x0nR11
R:2-165
2f
Gp_dh_N-2x0nR12
R:2-165
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