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2IYP
Asym. Unit
Info
Asym.Unit (237 KB)
Biol.Unit 1 (156 KB)
Biol.Unit 2 (155 KB)
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(1)
Title
:
PRODUCT RUP
Authors
:
R. Sundaramoorthy, J. Iulek, W. N. Hunter
Date
:
21 Jul 06 (Deposition) - 23 Jan 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.79
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C (2x)
Keywords
:
Oxidoreductase, 6-Phosphogluconate Dehydrogenase, Nadp, Pentose Shunt, Gluconate Utilization
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Sundaramoorthy, J. Iulek, M. P. Barrett, O. Bidet, G. F. Ruda, I. H. Gilbert, W. N. Hunter
Crystal Structures Of A Bacterial 6- Phosphogluconate Dehydrogenase Reveal Aspects Of Specificity, Mechanism And Mode Of Inhibition By Analogues Of High-Energy Reaction Intermediates.
Febs J. V. 274 275 2007
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Hetero Components
(3, 4)
Info
All Hetero Components
1a: RIBULOSE-5-PHOSPHATE (5RPa)
2a: ADENOSINE-2'-5'-DIPHOSPHATE (A2Pa)
2b: ADENOSINE-2'-5'-DIPHOSPHATE (A2Pb)
3a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
View:
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Label:
No.
Name
Count
Type
Full Name
1
5RP
1
Ligand/Ion
RIBULOSE-5-PHOSPHATE
2
A2P
2
Ligand/Ion
ADENOSINE-2'-5'-DIPHOSPHATE
3
NAP
1
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
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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 A:102 , LYS A:184 , HIS A:187 , ASN A:188 , GLU A:191 , TYR A:192 , LYS A:262 , THR A:264 , ARG A:289 , NAP A:1470 , HOH A:2034 , HOH A:2069 , HOH A:2136 , ARG B:447 , PHE B:450 , HIS B:453
BINDING SITE FOR RESIDUE 5RP A1471
2
AC2
SOFTWARE
GLY A:10 , MET A:11 , VAL A:13 , MET A:14 , ASN A:33 , ARG A:34 , THR A:35 , LYS A:38 , MET A:73 , VAL A:74 , GLN A:75 , ALA A:79 , GLY A:101 , ASN A:102 , VAL A:127 , GLY A:130 , LYS A:184 , 5RP A:1471 , HOH A:2034 , HOH A:2135 , HOH A:2136 , HOH A:2137 , GLY B:451
BINDING SITE FOR RESIDUE NAP A1470
3
AC3
SOFTWARE
GLY B:10 , MET B:11 , ALA B:12 , ASN B:33 , ARG B:34 , THR B:35 , LYS B:38 , VAL B:74 , GLN B:75 , ALA B:79 , HOH B:2134 , HOH B:2135 , HOH B:2136
BINDING SITE FOR RESIDUE A2P B1470
4
AC4
SOFTWARE
GLY C:10 , ASN C:33 , ARG C:34 , THR C:35 , LYS C:38 , VAL C:74 , GLN C:75 , ALA C:79 , THR C:83 , HOH C:2150 , HOH C:2151 , HOH C:2152
BINDING SITE FOR RESIDUE A2P C1470
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(1, 3)
Info
All PROSITE Patterns/Profiles
1: 6PGD (A:255-267,B:255-267,C:255-267)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
6PGD
PS00461
6-phosphogluconate dehydrogenase signature.
6PGD_LACLM
255-267
3
A:255-267
B:255-267
C:255-267
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Exons
(0, 0)
Info
All Exons
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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, 6)
Info
All SCOP Domains
1a: SCOP_d2iypa2 (A:178-470)
1b: SCOP_d2iypb2 (B:178-470)
1c: SCOP_d2iypc2 (C:178-470)
2a: SCOP_d2iypa1 (A:1-177)
2b: SCOP_d2iypb1 (B:0-177)
2c: SCOP_d2iypc1 (C:2-177)
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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)
Lactococcus lactis [TaxId: 1358]
(4)
1a
d2iypa2
A:178-470
1b
d2iypb2
B:178-470
1c
d2iypc2
C:178-470
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)
Lactococcus lactis [TaxId: 1358]
(4)
2a
d2iypa1
A:1-177
2b
d2iypb1
B:0-177
2c
d2iypc1
C:2-177
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CATH Domains
(3, 9)
Info
all CATH domains
1a: CATH_2iypB01 (B:0-181)
1b: CATH_2iypA01 (A:1-181)
1c: CATH_2iypC01 (C:2-181)
2a: CATH_2iypA02 (A:182-436)
2b: CATH_2iypB02 (B:182-436)
2c: CATH_2iypC02 (C:182-436)
3a: CATH_2iypA03 (A:437-470)
3b: CATH_2iypB03 (B:437-470)
3c: CATH_2iypC03 (C:437-470)
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Homologous Superfamilies
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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)
Lactococcus lactis. Organism_taxid: 1358. Strain: mg1363.
(4)
1a
2iypB01
B:0-181
1b
2iypA01
A:1-181
1c
2iypC01
C: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)
Lactococcus lactis. Organism_taxid: 1358. Strain: mg1363.
(4)
2a
2iypA02
A:182-436
2b
2iypB02
B:182-436
2c
2iypC02
C: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)
Lactococcus lactis. Organism_taxid: 1358. Strain: mg1363.
(4)
3a
2iypA03
A:437-470
3b
2iypB03
B:437-470
3c
2iypC03
C:437-470
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Asymmetric Unit 1
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select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
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show SS bonds with a radius of 100 units (=0.4Å)
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Asym.Unit (237 KB)
Header - Asym.Unit
Biol.Unit 1 (156 KB)
Header - Biol.Unit 1
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Header - Biol.Unit 2
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