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2GCG
Asym. Unit
Info
Asym.Unit (230 KB)
Biol.Unit 1 (111 KB)
Biol.Unit 2 (109 KB)
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(1)
Title
:
TERNARY CRYSTAL STRUCTURE OF HUMAN GLYOXYLATE REDUCTASE/HYDROXYPYRUVATE REDUCTASE
Authors
:
M. P. S. Booth, R. Conners, G. Rumsby, R. L. Brady
Date
:
14 Mar 06 (Deposition) - 18 Jul 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Nad(P) Rossmann Fold, Formate/Glycerate Dehydrogenase Substrate- Binding Domain, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. P. S. Booth, R. Conners, G. Rumsby, R. L. Brady
Structural Basis Of Substrate Specificity In Human Glyoxylate Reductase/Hydroxypyruvate Reductase
J. Mol. Biol. V. 360 178 2006
[
close entry info
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Hetero Components
(3, 11)
Info
All Hetero Components
1a: (2R)-2,3-DIHYDROXYPROPANOIC ACID (DGYa)
1b: (2R)-2,3-DIHYDROXYPROPANOIC ACID (DGYb)
2a: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPa)
2b: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPb)
2c: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPc)
2d: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPd)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DGY
2
Ligand/Ion
(2R)-2,3-DIHYDROXYPROPANOIC ACID
2
NDP
4
Ligand/Ion
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
3
SO4
5
Ligand/Ion
SULFATE ION
[
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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
GLY C:150 , THR C:152 , GLN C:153 , SER C:154 , ARG D:300
BINDING SITE FOR RESIDUE SO4 C 1001
02
AC2
SOFTWARE
ASP C:37 , LEU D:144 , SO4 D:1003
BINDING SITE FOR RESIDUE SO4 D 1002
03
AC3
SOFTWARE
ARG D:125 , LEU D:144 , TRP D:145 , LEU D:146 , SO4 D:1002 , HOH D:2033 , HOH D:2100 , HOH D:2120
BINDING SITE FOR RESIDUE SO4 D 1003
04
AC4
SOFTWARE
ARG C:300 , GLY D:150 , THR D:152 , GLN D:153 , SER D:154 , HOH D:2067
BINDING SITE FOR RESIDUE SO4 D 1004
05
AC5
SOFTWARE
ARG A:300 , GLY B:150 , THR B:152 , GLN B:153 , SER B:154
BINDING SITE FOR RESIDUE SO4 B 1005
06
AC6
SOFTWARE
VAL A:83 , THR A:111 , ILE A:159 , GLY A:160 , LEU A:161 , GLY A:162 , ARG A:163 , ILE A:164 , GLY A:184 , ARG A:185 , GLN A:186 , ARG A:188 , CYS A:216 , SER A:217 , THR A:222 , ILE A:243 , SER A:244 , ARG A:245 , ASP A:269 , HIS A:293 , GLY A:295 , SER A:296 , DGY A:3001 , HOH A:3003 , HOH A:3012 , HOH A:3021 , HOH A:3030 , HOH A:3169
BINDING SITE FOR RESIDUE NDP A 2001
07
AC7
SOFTWARE
VAL B:83 , THR B:111 , ILE B:159 , GLY B:160 , LEU B:161 , GLY B:162 , ARG B:163 , ILE B:164 , THR B:183 , GLY B:184 , ARG B:185 , GLN B:186 , ARG B:188 , ALA B:215 , CYS B:216 , SER B:217 , THR B:222 , ILE B:243 , SER B:244 , ARG B:245 , ASP B:269 , HIS B:293 , GLY B:295 , SER B:296 , HOH B:2008 , HOH B:2013 , HOH B:2023 , HOH B:2030 , HOH B:2035 , HOH B:2043 , HOH B:2045
BINDING SITE FOR RESIDUE NDP B 2002
08
AC8
SOFTWARE
VAL C:83 , THR C:111 , ILE C:159 , GLY C:160 , GLY C:162 , ARG C:163 , ILE C:164 , THR C:183 , GLY C:184 , ARG C:185 , ARG C:188 , ALA C:215 , CYS C:216 , SER C:217 , THR C:222 , ILE C:243 , SER C:244 , ARG C:245 , ASP C:269 , HIS C:293 , GLY C:295 , SER C:296 , DGY C:3002 , HOH C:3008 , HOH C:3012 , HOH C:3020 , HOH C:3022 , HOH C:3040 , HOH C:3078
BINDING SITE FOR RESIDUE NDP C 2003
09
AC9
SOFTWARE
VAL D:83 , THR D:111 , GLY D:162 , ARG D:163 , ILE D:164 , GLY D:184 , ARG D:185 , ARG D:188 , ALA D:215 , CYS D:216 , SER D:217 , THR D:222 , ILE D:243 , SER D:244 , ARG D:245 , ASP D:269 , HIS D:293 , GLY D:295 , SER D:296 , HOH D:2014 , HOH D:2096 , HOH D:2104 , HOH D:2107
BINDING SITE FOR RESIDUE NDP D 2004
10
BC1
SOFTWARE
LEU A:59 , SER A:82 , VAL A:83 , GLY A:84 , LEU A:107 , ARG A:245 , HIS A:293 , SER A:296 , NDP A:2001 , TRP B:141
BINDING SITE FOR RESIDUE DGY A 3001
11
BC2
SOFTWARE
LEU C:59 , SER C:82 , VAL C:83 , GLY C:84 , LEU C:107 , ARG C:245 , HIS C:293 , SER C:296 , NDP C:2003 , TRP D:141
BINDING SITE FOR RESIDUE DGY C 3002
[
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]
SAPs(SNPs)/Variants
(1, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_032762 (R170Q, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_032762
R
170
Q
GRHPR_HUMAN
Polymorphism
12002324
A/B/C/D
R
170
Q
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: D_2_HYDROXYACID_DH_3 (A:234-250,B:234-250,C:234-250,D:23...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
D_2_HYDROXYACID_DH_3
PS00671
D-isomer specific 2-hydroxyacid dehydrogenases signature 3.
GRHPR_HUMAN
234-250
4
A:234-250
B:234-250
C:234-250
D:234-250
[
close PROSITE info
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Exons
(9, 36)
Info
All Exons
Exon 1.1b (A:5-28 | B:6-28 | C:5-28 | D:6-28)
Exon 1.2 (A:28-72 | B:28-72 | C:28-72 | D:28...)
Exon 1.3a (A:72-96 | B:72-96 | C:72-96 | D:72...)
Exon 1.3c (A:96-135 | B:96-135 | C:96-135 | D...)
Exon 1.4b (A:135-165 | B:135-165 | C:135-165 ...)
Exon 1.4f (A:165-200 | B:165-200 | C:165-200 ...)
Exon 1.4h (A:200-245 | B:200-245 | C:200-245 ...)
Exon 1.4l (A:245-289 | B:245-289 | C:245-289 ...)
Exon 1.6e (A:289-328 | B:289-328 | C:289-328 ...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1b
02: Boundary 1.1b/1.2
03: Boundary 1.2/1.3a
04: Boundary 1.3a/1.3c
05: Boundary 1.3c/1.4b
06: Boundary 1.4b/1.4f
07: Boundary 1.4f/1.4h
08: Boundary 1.4h/1.4l
09: Boundary 1.4l/1.6e
10: Boundary 1.6e/-
View:
Label:
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
1.1b
ENST00000318158
1b
ENSE00001934486
chr9:
37422663-37422830
168
GRHPR_HUMAN
1-28
28
4
A:5-28
B:6-28
C:5-28
D:6-28
24
23
24
23
1.2
ENST00000318158
2
ENSE00001258021
chr9:
37424842-37424972
131
GRHPR_HUMAN
28-72
45
4
A:28-72
B:28-72
C:28-72
D:28-72
45
45
45
45
1.3a
ENST00000318158
3a
ENSE00001258055
chr9:
37425919-37425991
73
GRHPR_HUMAN
72-96
25
4
A:72-96
B:72-96
C:72-96
D:72-96
25
25
25
25
1.3c
ENST00000318158
3c
ENSE00001257930
chr9:
37426535-37426651
117
GRHPR_HUMAN
96-135
40
4
A:96-135
B:96-135
C:96-135
D:96-135
40
40
40
40
1.4b
ENST00000318158
4b
ENSE00001257990
chr9:
37428481-37428569
89
GRHPR_HUMAN
135-165
31
4
A:135-165
B:135-165
C:135-165
D:135-165
31
31
31
31
1.4f
ENST00000318158
4f
ENSE00001149947
chr9:
37429729-37429833
105
GRHPR_HUMAN
165-200
36
4
A:165-200
B:165-200
C:165-200
D:165-200
36
36
36
36
1.4h
ENST00000318158
4h
ENSE00001149942
chr9:
37430508-37430643
136
GRHPR_HUMAN
200-245
46
4
A:200-245
B:200-245
C:200-245
D:200-245
46
46
46
46
1.4l
ENST00000318158
4l
ENSE00000928324
chr9:
37432005-37432135
131
GRHPR_HUMAN
245-289
45
4
A:245-289
B:245-289
C:245-289
D:245-289
45
45
45
45
1.6e
ENST00000318158
6e
ENSE00001952551
chr9:
37436658-37436987
330
GRHPR_HUMAN
289-328
40
4
A:289-328
B:289-328
C:289-328
D:289-328
40
40
40
40
[
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]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
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Label:
Sorry, no Info available
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2gcgA02 (A:106-294)
1b: CATH_2gcgB02 (B:106-294)
1c: CATH_2gcgC02 (C:106-294)
1d: CATH_2gcgD02 (D:106-294)
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Classes
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(
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(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Human (Homo sapiens)
(188)
1a
2gcgA02
A:106-294
1b
2gcgB02
B:106-294
1c
2gcgC02
C:106-294
1d
2gcgD02
D:106-294
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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Asym.Unit (230 KB)
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