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1YWG
Asym. Unit
Info
Asym.Unit (221 KB)
Biol.Unit 1 (214 KB)
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(1)
Title
:
THE STRUCTURE OF GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM PLASMODIUM FALCIPARUM
Authors
:
J. F. Satchell, N. Klonis, R. L. Malby, A. Adisa, A. E. Alpyurek, P. M. Col L. Tilley
Date
:
17 Feb 05 (Deposition) - 29 Nov 05 (Release) - 12 Nov 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : O,P,Q,R
Biol. Unit 1: O,P,Q,R (1x)
Keywords
:
Rossmann Fold, Dehydrogenase, Tetrameric, Oxidoreductase
(Keyword Search:
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Reference
:
J. F. Satchell, R. L. Malby, C. S. Luo, A. Adisa, A. E. Alpyurek, N. Klonis, B. J. Smith, L. Tilley, P. M. Colman
Structure Of Glyceraldehyde-3-Phosphate Dehydrogenase From Plasmodium Falciparum.
Acta Crystallogr. , Sect. D V. 61 1213 2005
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Hetero Components
(1, 4)
Info
All Hetero Components
1a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
1b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
1c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
1d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
View:
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Label:
No.
Name
Count
Type
Full Name
1
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:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN O:9 , GLY O:10 , PHE O:11 , GLY O:12 , ARG O:13 , ILE O:14 , ASN O:34 , ASP O:35 , PRO O:36 , PHE O:37 , GLU O:79 , LYS O:80 , SER O:98 , THR O:99 , PHE O:102 , SER O:122 , ALA O:123 , CYS O:153 , THR O:183 , ALA O:184 , ASN O:319 , TYR O:323 , HOH O:406 , HOH O:415 , HOH O:469 , HOH O:541 , HOH O:544 , HOH O:586 , HOH O:639 , HOH O:659 , HOH O:700
BINDING SITE FOR RESIDUE NAD O 401
2
AC2
SOFTWARE
ASN P:9 , GLY P:10 , PHE P:11 , GLY P:12 , ARG P:13 , ILE P:14 , ASN P:34 , ASP P:35 , PRO P:36 , PHE P:37 , GLU P:79 , LYS P:80 , SER P:98 , THR P:99 , PHE P:102 , SER P:122 , ALA P:123 , CYS P:153 , ALA P:184 , ASN P:319 , TYR P:323 , HOH P:492 , HOH P:493 , HOH P:563 , HOH P:665 , HOH P:711
BINDING SITE FOR RESIDUE NAD P 402
3
AC3
SOFTWARE
HOH P:655 , ASN Q:9 , GLY Q:10 , PHE Q:11 , GLY Q:12 , ARG Q:13 , ILE Q:14 , ASN Q:34 , ASP Q:35 , PRO Q:36 , PHE Q:37 , GLU Q:79 , LYS Q:80 , SER Q:98 , THR Q:99 , PHE Q:102 , SER Q:122 , ALA Q:123 , CYS Q:153 , ALA Q:184 , ASN Q:319 , TYR Q:323 , HOH Q:429 , HOH Q:436 , HOH Q:498 , HOH Q:511 , HOH Q:716 , HOH Q:831
BINDING SITE FOR RESIDUE NAD Q 403
4
AC4
SOFTWARE
ASN R:9 , GLY R:10 , PHE R:11 , GLY R:12 , ARG R:13 , ILE R:14 , ASN R:34 , ASP R:35 , PRO R:36 , PHE R:37 , GLU R:79 , LYS R:80 , SER R:98 , THR R:99 , PHE R:102 , SER R:122 , ALA R:123 , CYS R:153 , ALA R:184 , ASN R:319 , TYR R:323 , HOH R:442 , HOH R:471 , HOH R:577 , HOH R:734 , HOH R:736 , HOH R:789
BINDING SITE FOR RESIDUE NAD R 404
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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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.
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1ywgo2 (O:153-318)
1b: SCOP_d1ywgq2 (Q:153-318)
1c: SCOP_d1ywgr2 (R:153-318)
1d: SCOP_d1ywgp2 (P:153-318)
2a: SCOP_d1ywgo1 (O:1-152,O:319-337)
2b: SCOP_d1ywgq1 (Q:1-152,Q:319-337)
2c: SCOP_d1ywgr1 (R:1-152,R:319-337)
2d: SCOP_d1ywgp1 (P:1-152,P:319-337)
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)
(
)
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)
Malaria parasite (Plasmodium falciparum) [TaxId: 5833]
(3)
1a
d1ywgo2
O:153-318
1b
d1ywgq2
Q:153-318
1c
d1ywgr2
R:153-318
1d
d1ywgp2
P:153-318
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)
Malaria parasite (Plasmodium falciparum) [TaxId: 5833]
(3)
2a
d1ywgo1
O:1-152,O:319-337
2b
d1ywgq1
Q:1-152,Q:319-337
2c
d1ywgr1
R:1-152,R:319-337
2d
d1ywgp1
P:1-152,P:319-337
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1ywgO02 (O:151-319)
1b: CATH_1ywgQ02 (Q:151-319)
1c: CATH_1ywgR02 (R:151-319)
1d: CATH_1ywgP02 (P:151-319)
2a: CATH_1ywgO01 (O:1-150,O:320-337)
2b: CATH_1ywgP01 (P:1-150,P:320-337)
2c: CATH_1ywgQ01 (Q:1-150,Q:320-337)
2d: CATH_1ywgR01 (R:1-150,R:320-337)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Dihydrodipicolinate Reductase; domain 2
(182)
Homologous Superfamily
:
Dihydrodipicolinate Reductase; domain 2
(178)
Malaria parasite p (Plasmodium falciparum)
(3)
1a
1ywgO02
O:151-319
1b
1ywgQ02
Q:151-319
1c
1ywgR02
R:151-319
1d
1ywgP02
P:151-319
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Malaria parasite p (Plasmodium falciparum)
(33)
2a
1ywgO01
O:1-150,O:320-337
2b
1ywgP01
P:1-150,P:320-337
2c
1ywgQ01
Q:1-150,Q:320-337
2d
1ywgR01
R:1-150,R:320-337
[
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Gp_dh_C_1ywgR01 (R:158-317)
1b: PFAM_Gp_dh_C_1ywgR02 (R:158-317)
1c: PFAM_Gp_dh_C_1ywgR03 (R:158-317)
1d: PFAM_Gp_dh_C_1ywgR04 (R:158-317)
2a: PFAM_Gp_dh_N_1ywgR05 (R:4-153)
2b: PFAM_Gp_dh_N_1ywgR06 (R:4-153)
2c: PFAM_Gp_dh_N_1ywgR07 (R:4-153)
2d: PFAM_Gp_dh_N_1ywgR08 (R:4-153)
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Clans
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)
(
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Families
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)
(
)
Organisms
(
)
(
)
Clan
:
GADPH_aa-bio_dh
(59)
Family
:
Gp_dh_C
(38)
Plasmodium falciparum
(1)
1a
Gp_dh_C-1ywgR01
R:158-317
1b
Gp_dh_C-1ywgR02
R:158-317
1c
Gp_dh_C-1ywgR03
R:158-317
1d
Gp_dh_C-1ywgR04
R:158-317
Clan
:
NADP_Rossmann
(1239)
Family
:
Gp_dh_N
(38)
Plasmodium falciparum
(1)
2a
Gp_dh_N-1ywgR05
R:4-153
2b
Gp_dh_N-1ywgR06
R:4-153
2c
Gp_dh_N-1ywgR07
R:4-153
2d
Gp_dh_N-1ywgR08
R:4-153
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