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2JKV
Biol. Unit 1
Info
Asym.Unit (978 KB)
Biol.Unit 1 (327 KB)
Biol.Unit 2 (325 KB)
Biol.Unit 3 (321 KB)
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(1)
Title
:
STRUCTURE OF HUMAN PHOSPHOGLUCONATE DEHYDROGENASE IN COMPLEX WITH NADPH AT 2.53A
Authors
:
E. S. Pilka, K. L. Kavanagh, F. Von Delft, J. R. C. Muniz, J. Murray, S. Pi K. Guo, A. Edwards, C. H. Arrowsmith, J. Weigelt, C. Bountra, U. Opperm
Date
:
01 Sep 08 (Deposition) - 01 Sep 09 (Release) - 14 Jan 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.53
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Keywords
:
Oxidoreductase, Phosphogluconate, Nadp, Nadph, Pentose Shunt, Dehydrogenase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. S. Ng, F. Von Delft, E. S. Pilka, K. L. Kavanagh, M. A. Mcdonough, P. Savitsky, C. H. Arrowsmith, J. Weigelt, A. Edwards, M. Sundstrom, C. J. Schofield, U. Oppermann
Structure Of Human Phosphogluconate Dehydrogenase In Complex With Nadph At 2. 53A
To Be Published
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Hetero Components
(2, 6)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
1e: CHLORIDE ION (CLe)
1f: CHLORIDE ION (CLf)
1g: CHLORIDE ION (CLg)
1h: CHLORIDE ION (CLh)
1i: CHLORIDE ION (CLi)
1j: CHLORIDE ION (CLj)
1k: CHLORIDE ION (CLk)
2a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
2b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
2c: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPc)
2d: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPd)
2e: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPe)
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)
3h: SULFATE ION (SO4h)
3i: SULFATE ION (SO4i)
3j: SULFATE ION (SO4j)
3k: SULFATE ION (SO4k)
3l: SULFATE ION (SO4l)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
-1
Ligand/Ion
CHLORIDE ION
2
NAP
2
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
3
SO4
4
Ligand/Ion
SULFATE ION
[
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Sites
(12, 12)
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: CC5 (SOFTWARE)
11: CC7 (SOFTWARE)
12: CC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:451 , HIS A:453 , SER A:478 , SER A:479 , TYR A:481 , HOH A:2252 , HOH A:2253 , HOH A:2254 , HOH A:2255 , HOH A:2256 , HOH A:2257 , HOH A:2258 , GLY B:10 , LEU B:11 , ALA B:12 , VAL B:13 , MET B:14 , ASN B:33 , ARG B:34 , THR B:35 , LYS B:38 , LEU B:74 , VAL B:75 , LYS B:76 , ALA B:77 , ALA B:80 , PHE B:84 , GLY B:102 , ASN B:103 , VAL B:128 , GLY B:131 , CL B:1484 , HOH B:2046 , HOH B:2049
BINDING SITE FOR RESIDUE NAP A 500
02
AC2
SOFTWARE
ASN A:103 , LYS A:184 , ASN A:188 , NAP B:500
BINDING SITE FOR RESIDUE CL A1484
03
AC3
SOFTWARE
TYR A:192 , GLN A:260 , LYS A:261 , ARG A:288 , HOH A:2160 , HOH A:2259 , HOH A:2260 , HOH A:2261 , ARG B:447 , HIS B:453
BINDING SITE FOR RESIDUE SO4 A1485
04
AC4
SOFTWARE
LYS A:248 , HIS A:249 , HOH A:2262 , HOH A:2263
BINDING SITE FOR RESIDUE SO4 A1486
05
AC5
SOFTWARE
GLY A:10 , LEU A:11 , ALA A:12 , VAL A:13 , MET A:14 , ASN A:33 , ARG A:34 , THR A:35 , LYS A:38 , LEU A:74 , VAL A:75 , LYS A:76 , ALA A:77 , ALA A:80 , PHE A:84 , GLY A:102 , ASN A:103 , VAL A:128 , GLY A:131 , CL A:1484 , HOH A:2014 , HOH A:2039 , GLY B:451 , SER B:478 , SER B:479 , TYR B:481 , HOH B:2262 , HOH B:2263 , HOH B:2264 , HOH B:2265
BINDING SITE FOR RESIDUE NAP B 500
06
AC6
SOFTWARE
NAP A:500 , ASN B:103 , LYS B:184 , ASN B:188
BINDING SITE FOR RESIDUE CL B1484
07
AC7
SOFTWARE
TRP B:150 , LYS B:154
BINDING SITE FOR RESIDUE CL B1485
08
AC8
SOFTWARE
ARG A:447 , TYR B:192 , GLN B:260 , LYS B:261 , ARG B:288 , HOH B:2165 , HOH B:2266 , HOH B:2267
BINDING SITE FOR RESIDUE SO4 B1486
09
AC9
SOFTWARE
LYS B:248 , HIS B:249 , HOH B:2158 , HOH B:2269
BINDING SITE FOR RESIDUE SO4 B1487
10
CC5
SOFTWARE
LYS A:303
BINDING SITE FOR RESIDUE CL A1488
11
CC7
SOFTWARE
TRP A:150 , LYS A:154 , ASP A:172 , HOH A:2096
BINDING SITE FOR RESIDUE CL A1487
12
CC8
SOFTWARE
LYS B:303 , HOH B:2174
BINDING SITE FOR RESIDUE CL B1488
[
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]
SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_048104 (A268S, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_048104
A
268
S
6PGD_HUMAN
Polymorphism
11547610
A/B
A
268
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: 6PGD (A:254-266,B:254-266)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
6PGD
PS00461
6-phosphogluconate dehydrogenase signature.
6PGD_HUMAN
254-266
2
A:254-266
B:254-266
-
-
-
-
[
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Exons
(0, 0)
Info
All Exons
View:
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Label:
All Exon Boundaries
View:
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_d2jkva2 (A:178-483)
1b: SCOP_d2jkve2 (E:178-483)
1c: SCOP_d2jkvf2 (F:178-472)
1d: SCOP_d2jkvb2 (B:178-483)
1e: SCOP_d2jkvc2 (C:178-483)
1f: SCOP_d2jkvd2 (D:178-483)
2a: SCOP_d2jkva1 (A:2-177)
2b: SCOP_d2jkvb1 (B:2-177)
2c: SCOP_d2jkvc1 (C:2-177)
2d: SCOP_d2jkvd1 (D:2-177)
2e: SCOP_d2jkve1 (E:2-177)
2f: SCOP_d2jkvf1 (F:2-177)
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)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
d2jkva2
A:178-483
1b
d2jkve2
E:178-483
1c
d2jkvf2
F:178-472
1d
d2jkvb2
B:178-483
1e
d2jkvc2
C:178-483
1f
d2jkvd2
D:178-483
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
d2jkva1
A:2-177
2b
d2jkvb1
B:2-177
2c
d2jkvc1
C:2-177
2d
d2jkvd1
D:2-177
2e
d2jkve1
E:2-177
2f
d2jkvf1
F:2-177
[
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]
CATH Domains
(3, 17)
Info
all CATH domains
1a: CATH_2jkvA01 (A:2-181)
1b: CATH_2jkvF01 (F:2-181)
1c: CATH_2jkvB01 (B:2-181)
1d: CATH_2jkvC01 (C:2-181)
1e: CATH_2jkvD01 (D:2-181)
1f: CATH_2jkvE01 (E:2-181)
2a: CATH_2jkvA02 (A:182-436)
2b: CATH_2jkvB02 (B:182-436)
2c: CATH_2jkvC02 (C:182-436)
2d: CATH_2jkvD02 (D:182-436)
2e: CATH_2jkvE02 (E:182-436)
2f: CATH_2jkvF02 (F:182-436)
3a: CATH_2jkvA03 (A:437-483)
3b: CATH_2jkvB03 (B:437-483)
3c: CATH_2jkvC03 (C:437-483)
3d: CATH_2jkvD03 (D:437-483)
3e: CATH_2jkvE03 (E:437-483)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
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
2jkvA01
A:2-181
1b
2jkvF01
F:2-181
1c
2jkvB01
B:2-181
1d
2jkvC01
C:2-181
1e
2jkvD01
D:2-181
1f
2jkvE01
E:2-181
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)
Human (Homo sapiens)
(12)
2a
2jkvA02
A:182-436
2b
2jkvB02
B:182-436
2c
2jkvC02
C:182-436
2d
2jkvD02
D:182-436
2e
2jkvE02
E:182-436
2f
2jkvF02
F:182-436
Architecture
:
Up-down Bundle
(3216)
Topology
:
Single alpha-helices involved in coiled-coils or other helix-helix interfaces
(552)
Homologous Superfamily
:
6-Phosphogluconate Dehydrogenase, domain 3
(20)
Human (Homo sapiens)
(1)
3a
2jkvA03
A:437-483
3b
2jkvB03
B:437-483
3c
2jkvC03
C:437-483
3d
2jkvD03
D:437-483
3e
2jkvE03
E:437-483
[
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]
Pfam Domains
(2, 12)
Info
all PFAM domains
1a: PFAM_6PGD_2jkvF01 (F:180-470)
1b: PFAM_6PGD_2jkvF02 (F:180-470)
1c: PFAM_6PGD_2jkvF03 (F:180-470)
1d: PFAM_6PGD_2jkvF04 (F:180-470)
1e: PFAM_6PGD_2jkvF05 (F:180-470)
1f: PFAM_6PGD_2jkvF06 (F:180-470)
2a: PFAM_NAD_binding_2_2jkvF07 (F:3-176)
2b: PFAM_NAD_binding_2_2jkvF08 (F:3-176)
2c: PFAM_NAD_binding_2_2jkvF09 (F:3-176)
2d: PFAM_NAD_binding_2_2jkvF10 (F:3-176)
2e: PFAM_NAD_binding_2_2jkvF11 (F:3-176)
2f: PFAM_NAD_binding_2_2jkvF12 (F:3-176)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
6PGD_C
(47)
Family
:
6PGD
(10)
Homo sapiens (Human)
(1)
1a
6PGD-2jkvF01
F:180-470
1b
6PGD-2jkvF02
F:180-470
1c
6PGD-2jkvF03
F:180-470
1d
6PGD-2jkvF04
F:180-470
1e
6PGD-2jkvF05
F:180-470
1f
6PGD-2jkvF06
F:180-470
Clan
:
NADP_Rossmann
(1239)
Family
:
NAD_binding_2
(15)
Homo sapiens (Human)
(2)
2a
NAD_binding_2-2jkvF07
F:3-176
2b
NAD_binding_2-2jkvF08
F:3-176
2c
NAD_binding_2-2jkvF09
F:3-176
2d
NAD_binding_2-2jkvF10
F:3-176
2e
NAD_binding_2-2jkvF11
F:3-176
2f
NAD_binding_2-2jkvF12
F:3-176
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