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1WPQ
Asym. Unit
Info
Asym.Unit (110 KB)
Biol.Unit 1 (106 KB)
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(1)
Title
:
TERNARY COMPLEX OF GLYCEROL 3-PHOSPHATE DEHYDROGENASE 1 WITH NAD AND DIHYDROXYACTONE
Authors
:
X. Ou, X. Han, Z. Rao
Date
:
10 Sep 04 (Deposition) - 11 Apr 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Nad, Gpd1, Dehydrogenase, Dihydroxyactone Complex, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
X. Ou, C. Ji, X. Han, X. Zhao, X. Li, Y. Mao, L. L. Wong, M. Bartlam, Z. Rao
Crystal Structures Of Human Glycerol 3-Phosphate Dehydrogenase 1 (Gpd1)
J. Mol. Biol. V. 357 858 2006
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 11)
Info
All Hetero Components
1a: 1,3-DIHYDROXYACETONEPHOSPHATE (13Pa)
1b: 1,3-DIHYDROXYACETONEPHOSPHATE (13Pb)
2a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
2b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
13P
2
Ligand/Ion
1,3-DIHYDROXYACETONEPHOSPHATE
2
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3
SO4
7
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(11, 11)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS A:20 , GLY A:66 , HIS A:67 , LYS A:68 , HOH A:3042 , HOH A:3047 , HOH A:3135 , HOH A:3175 , HOH A:3245
BINDING SITE FOR RESIDUE SO4 A 1001
02
AC2
SOFTWARE
HOH A:3132 , HOH A:3195 , HOH A:3293 , LYS B:20 , HIS B:67 , LYS B:68
BINDING SITE FOR RESIDUE SO4 A 1002
03
AC3
SOFTWARE
ARG A:271 , LYS A:272 , HOH A:3214
BINDING SITE FOR RESIDUE SO4 A 1003
04
AC4
SOFTWARE
LYS A:178 , GLN A:182 , ARG A:187 , HOH A:3102 , HOH A:3256
BINDING SITE FOR RESIDUE SO4 A 1004
05
AC5
SOFTWARE
LYS B:240 , VAL B:247 , SER B:248 , SER B:249 , HOH B:3102
BINDING SITE FOR RESIDUE SO4 B 1005
06
AC6
SOFTWARE
VAL A:247 , SER A:248 , HOH A:3003 , HOH A:3033 , HOH A:3288
BINDING SITE FOR RESIDUE SO4 A 1006
07
AC7
SOFTWARE
PRO A:346 , GLU A:347 , HIS A:348 , HOH A:3101 , HOH A:3149
BINDING SITE FOR RESIDUE SO4 A 1007
08
AC8
SOFTWARE
LYS B:120 , LYS B:204 , ASN B:205 , THR B:264 , GLY B:268 , ARG B:269 , ASN B:270 , NAD B:3002 , HOH B:3012 , HOH B:3013 , HOH B:3161 , HOH B:3191
BINDING SITE FOR RESIDUE 13P B 2001
09
AC9
SOFTWARE
LYS A:120 , GLY A:149 , LYS A:204 , ASN A:205 , ASP A:260 , THR A:264 , GLY A:268 , ARG A:269 , ASN A:270 , NAD A:3001 , HOH A:3005 , HOH A:3037 , HOH A:3058 , HOH A:3136 , HOH A:3197
BINDING SITE FOR RESIDUE 13P A 2002
10
BC1
SOFTWARE
SER A:11 , GLY A:12 , ASN A:13 , TRP A:14 , GLY A:15 , PHE A:41 , TYR A:63 , VAL A:92 , PRO A:94 , PHE A:97 , LEU A:118 , LYS A:120 , ASN A:151 , ILE A:152 , ALA A:153 , ARG A:269 , GLY A:294 , GLN A:295 , LYS A:296 , GLN A:298 , 13P A:2002 , HOH A:3026 , HOH A:3038 , HOH A:3054 , HOH A:3056 , HOH A:3058 , HOH A:3197
BINDING SITE FOR RESIDUE NAD A 3001
11
BC2
SOFTWARE
SER B:11 , GLY B:12 , ASN B:13 , TRP B:14 , GLY B:15 , PHE B:41 , TYR B:63 , VAL B:93 , PRO B:94 , PHE B:97 , LEU B:118 , ILE B:119 , LYS B:120 , ASN B:151 , ILE B:152 , ALA B:153 , ARG B:269 , GLY B:294 , GLN B:295 , LYS B:296 , GLN B:298 , 13P B:2001 , HOH B:3011 , HOH B:3013 , HOH B:3020 , HOH B:3023 , HOH B:3037 , HOH B:3120
BINDING SITE FOR RESIDUE NAD B 3002
[
close Site info
]
SAPs(SNPs)/Variants
(6, 12)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_029492 (I54V, chain A/B, )
2: VAR_029493 (P113P, chain A/B, )
3: VAR_067425 (E124K, chain A/B, )
4: VAR_049220 (V197A, chain A/B, )
5: VAR_067426 (T223I, chain A/B, )
6: VAR_071967 (R229P, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_029492
I
54
V
GPDA_HUMAN
Polymorphism
2232202
A/B
I
54
V
2
UniProt
VAR_029493
A
113
P
GPDA_HUMAN
Polymorphism
1128867
A/B
P
113
P
3
UniProt
VAR_067425
E
124
K
GPDA_HUMAN
Polymorphism
34783513
A/B
E
124
K
4
UniProt
VAR_049220
V
197
A
GPDA_HUMAN
Polymorphism
2232207
A/B
V
197
A
5
UniProt
VAR_067426
T
223
I
GPDA_HUMAN
Polymorphism
---
A/B
T
223
I
6
UniProt
VAR_071967
R
229
P
GPDA_HUMAN
Disease (HTGTI)
---
A/B
R
229
P
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: NAD_G3PDH (A:201-222,B:201-222)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
NAD_G3PDH
PS00957
NAD-dependent glycerol-3-phosphate dehydrogenase signature.
GPDA_HUMAN
201-222
2
A:201-222
B:201-222
[
close PROSITE info
]
Exons
(8, 16)
Info
All Exons
Exon 1.1 (A:2-14 | B:2-14)
Exon 1.2 (A:14-73 | B:14-73)
Exon 1.3 (A:74-120 | B:74-120)
Exon 1.4 (A:121-167 | B:121-167)
Exon 1.5 (A:167-204 | B:167-204)
Exon 1.6 (A:205-282 | B:205-282)
Exon 1.7 (A:283-318 | B:283-318)
Exon 1.8 (A:318-349 | B:318-349)
View:
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All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/1.2
3: Boundary 1.2/1.3
4: Boundary 1.3/1.4
5: Boundary 1.4/1.5
6: Boundary 1.5/1.6
7: Boundary 1.6/1.7
8: Boundary 1.7/1.8
9: Boundary 1.8/-
View:
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENST00000301149
1
ENSE00001239163
chr12:
50497801-50497874
74
GPDA_HUMAN
1-14
14
2
A:2-14
B:2-14
13
13
1.2
ENST00000301149
2
ENSE00001194139
chr12:
50498357-50498534
178
GPDA_HUMAN
14-73
60
2
A:14-73
B:14-73
60
60
1.3
ENST00000301149
3
ENSE00001194132
chr12:
50499331-50499471
141
GPDA_HUMAN
74-120
47
2
A:74-120
B:74-120
47
47
1.4
ENST00000301149
4
ENSE00001680723
chr12:
50500071-50500209
139
GPDA_HUMAN
121-167
47
2
A:121-167
B:121-167
47
47
1.5
ENST00000301149
5
ENSE00001194124
chr12:
50500588-50500700
113
GPDA_HUMAN
167-204
38
2
A:167-204
B:167-204
38
38
1.6
ENST00000301149
6
ENSE00001728210
chr12:
50501350-50501583
234
GPDA_HUMAN
205-282
78
2
A:205-282
B:205-282
78
78
1.7
ENST00000301149
7
ENSE00001194116
chr12:
50501807-50501913
107
GPDA_HUMAN
283-318
36
2
A:283-318
B:283-318
36
36
1.8
ENST00000301149
8
ENSE00001239159
chr12:
50503206-50505091
1886
GPDA_HUMAN
318-349
32
2
A:318-349
B:318-349
32
32
[
close EXON info
]
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1wpqa2 (A:194-349)
1b: SCOP_d1wpqb2 (B:194-349)
2a: SCOP_d1wpqa1 (A:2-193)
2b: SCOP_d1wpqb1 (B:2-193)
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)
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)
Protein Domains
(
)
(
)
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
:
automated matches
(50)
Protein domain
:
automated matches
(50)
Human (Homo sapiens) [TaxId: 9606]
(13)
1a
d1wpqa2
A:194-349
1b
d1wpqb2
B:194-349
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
:
automated matches
(447)
Protein domain
:
automated matches
(447)
Human (Homo sapiens) [TaxId: 9606]
(32)
2a
d1wpqa1
A:2-193
2b
d1wpqb1
B:2-193
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_NAD_Gly3P_dh_C_1wpqB01 (B:192-342)
1b: PFAM_NAD_Gly3P_dh_C_1wpqB02 (B:192-342)
2a: PFAM_NAD_Gly3P_dh_N_1wpqB03 (B:5-174)
2b: PFAM_NAD_Gly3P_dh_N_1wpqB04 (B:5-174)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
6PGD_C
(47)
Family
:
NAD_Gly3P_dh_C
(11)
Homo sapiens (Human)
(4)
1a
NAD_Gly3P_dh_C-1wpqB01
B:192-342
1b
NAD_Gly3P_dh_C-1wpqB02
B:192-342
Clan
:
NADP_Rossmann
(1239)
Family
:
NAD_Gly3P_dh_N
(11)
Homo sapiens (Human)
(4)
2a
NAD_Gly3P_dh_N-1wpqB03
B:5-174
2b
NAD_Gly3P_dh_N-1wpqB04
B:5-174
[
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