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1N1E
Asym. Unit
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Asym.Unit (120 KB)
Biol.Unit 1 (114 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF LEISHMANIA MEXICANA GLYCEROL-3-PHOSPHATE DEHYDROGENASE COMPLEXED WITH DHAP AND NAD
Authors
:
J. Choe, W. G. J. Hol
Date
:
17 Oct 02 (Deposition) - 27 May 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Nad Binding Domain, Oxidoreductase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
J. Choe, D. Guerra, P. A. M. Michels, W. G. J. Hol
Leishmania Mexicana Glycerol-3-Phosphate Dehydrogenase Showed Conformational Changes Upon Binding A Bi-Substrate Adduct
J. Mol. Biol. V. 320 335 2003
(for further references see the
PDB file header
)
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: ADENOSINE 5'-(TRIHYDROGEN DIPHOSPH... (NDEa)
1b: ADENOSINE 5'-(TRIHYDROGEN DIPHOSPH... (NDEb)
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No.
Name
Count
Type
Full Name
1
NDE
2
Ligand/Ion
ADENOSINE 5'-(TRIHYDROGEN DIPHOSPHATE) P'-5'-ESTERWITH 3-(AMINOCARBONYL)-4-(1-HYDROXYL-2-OXO-3-PHOSPHONOOXY-PROPYL)-1-BETA-D-RIBOFURANOSYLPYRIDINIUMINNER SALT
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SER A:23 , GLY A:24 , ALA A:25 , PHE A:26 , HIS A:45 , MET A:46 , PHE A:63 , VAL A:92 , PRO A:94 , PHE A:97 , THR A:124 , LYS A:125 , GLY A:153 , SER A:155 , PHE A:156 , ALA A:157 , LYS A:210 , ASN A:211 , THR A:267 , SER A:273 , ARG A:274 , ASN A:275 , ALA A:297 , VAL A:298 , GLU A:300 , HOH A:428 , HOH A:460 , HOH A:463 , HOH A:466 , HOH A:467 , HOH A:469 , HOH A:471 , HOH A:486 , HOH A:525 , HOH A:535
BINDING SITE FOR RESIDUE NDE A 400
2
AC2
SOFTWARE
SER B:23 , GLY B:24 , ALA B:25 , PHE B:26 , HIS B:45 , PHE B:63 , VAL B:92 , PRO B:94 , PHE B:97 , THR B:124 , LYS B:125 , GLY B:153 , SER B:155 , PHE B:156 , ALA B:157 , LYS B:210 , ASN B:211 , THR B:267 , SER B:273 , ARG B:274 , ASN B:275 , ALA B:297 , VAL B:298 , GLU B:300 , HOH B:417 , HOH B:468 , HOH B:473 , HOH B:475 , HOH B:479 , HOH B:525 , HOH B:560
BINDING SITE FOR RESIDUE NDE B 401
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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
(1, 2)
Info
All PROSITE Patterns/Profiles
1: NAD_G3PDH (A:207-228,B:207-228)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
NAD_G3PDH
PS00957
NAD-dependent glycerol-3-phosphate dehydrogenase signature.
GPDA_LEIME
207-228
2
A:207-228
B:207-228
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1n1ea1 (A:198-357)
1b: SCOP_d1n1eb1 (B:198-357)
2a: SCOP_d1n1ea2 (A:9-197)
2b: SCOP_d1n1eb2 (B:9-197)
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Protein Domains
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)
(
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Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
6-phosphogluconate dehydrogenase C-terminal domain-like
(119)
Superfamily
:
6-phosphogluconate dehydrogenase C-terminal domain-like
(119)
Family
:
Glycerol-3-phosphate dehydrogenase
(8)
Protein domain
:
Glycerol-3-phosphate dehydrogenase
(8)
Trypanosome (Leishmania mexicana) [TaxId: 5665]
(7)
1a
d1n1ea1
A:198-357
1b
d1n1eb1
B:198-357
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
:
6-phosphogluconate dehydrogenase-like, N-terminal domain
(69)
Protein domain
:
Glycerol-3- phosphate dehydrogenase
(8)
Trypanosome (Leishmania mexicana) [TaxId: 5665]
(7)
2a
d1n1ea2
A:9-197
2b
d1n1eb2
B:9-197
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1n1eA01 (A:9-206)
1b: CATH_1n1eB01 (B:9-206)
2a: CATH_1n1eA02 (A:208-356)
2b: CATH_1n1eB02 (B:208-356)
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)
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)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Leishmania mexicana. Organism_taxid: 5665.
(8)
1a
1n1eA01
A:9-206
1b
1n1eB01
B:9-206
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
(60)
Homologous Superfamily
:
N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
(59)
Leishmania mexicana. Organism_taxid: 5665.
(6)
2a
1n1eA02
A:208-356
2b
1n1eB02
B:208-356
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_NAD_Gly3P_dh_C_1n1eB01 (B:198-342)
1b: PFAM_NAD_Gly3P_dh_C_1n1eB02 (B:198-342)
2a: PFAM_NAD_Gly3P_dh_N_1n1eB03 (B:17-178)
2b: PFAM_NAD_Gly3P_dh_N_1n1eB04 (B:17-178)
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Clan
:
6PGD_C
(47)
Family
:
NAD_Gly3P_dh_C
(11)
Leishmania mexicana
(4)
1a
NAD_Gly3P_dh_C-1n1eB01
B:198-342
1b
NAD_Gly3P_dh_C-1n1eB02
B:198-342
Clan
:
NADP_Rossmann
(1239)
Family
:
NAD_Gly3P_dh_N
(11)
Leishmania mexicana
(4)
2a
NAD_Gly3P_dh_N-1n1eB03
B:17-178
2b
NAD_Gly3P_dh_N-1n1eB04
B:17-178
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