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1JVS
Asym. Unit
Info
Asym.Unit (139 KB)
Biol.Unit 1 (132 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE; A TARGET ENZYME FOR ANTIMALARIAL DRUGS
Authors
:
S. Yajima, T. Nonaka, T. Kuzuyama, H. Seto, K. Ohsawa
Date
:
31 Aug 01 (Deposition) - 09 Oct 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Reductoisomerase, Nadph, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Yajima, T. Nonaka, T. Kuzuyama, H. Seto, K. Ohsawa
Crystal Structure Of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase Complexed With Cofactors: Implications Of A Flexible Loop Movement Upon Substrate Binding.
J. Biochem. (Tokyo) V. 131 313 2002
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 40)
Info
All Hetero Components
1a: SELENOMETHIONINE (MSEa)
1aa: SELENOMETHIONINE (MSEaa)
1ab: SELENOMETHIONINE (MSEab)
1ac: SELENOMETHIONINE (MSEac)
1ad: SELENOMETHIONINE (MSEad)
1ae: SELENOMETHIONINE (MSEae)
1af: SELENOMETHIONINE (MSEaf)
1ag: SELENOMETHIONINE (MSEag)
1ah: SELENOMETHIONINE (MSEah)
1ai: SELENOMETHIONINE (MSEai)
1aj: SELENOMETHIONINE (MSEaj)
1b: SELENOMETHIONINE (MSEb)
1c: SELENOMETHIONINE (MSEc)
1d: SELENOMETHIONINE (MSEd)
1e: SELENOMETHIONINE (MSEe)
1f: SELENOMETHIONINE (MSEf)
1g: SELENOMETHIONINE (MSEg)
1h: SELENOMETHIONINE (MSEh)
1i: SELENOMETHIONINE (MSEi)
1j: SELENOMETHIONINE (MSEj)
1k: SELENOMETHIONINE (MSEk)
1l: SELENOMETHIONINE (MSEl)
1m: SELENOMETHIONINE (MSEm)
1n: SELENOMETHIONINE (MSEn)
1o: SELENOMETHIONINE (MSEo)
1p: SELENOMETHIONINE (MSEp)
1q: SELENOMETHIONINE (MSEq)
1r: SELENOMETHIONINE (MSEr)
1s: SELENOMETHIONINE (MSEs)
1t: SELENOMETHIONINE (MSEt)
1u: SELENOMETHIONINE (MSEu)
1v: SELENOMETHIONINE (MSEv)
1w: SELENOMETHIONINE (MSEw)
1x: SELENOMETHIONINE (MSEx)
1y: SELENOMETHIONINE (MSEy)
1z: SELENOMETHIONINE (MSEz)
2a: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPa)
2b: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPb)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MSE
36
Mod. Amino Acid
SELENOMETHIONINE
2
NDP
2
Ligand/Ion
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
3
SO4
2
Ligand/Ion
SULFATE ION
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY A:184 , SER A:185 , HIS A:208 , SER A:221 , ASN A:226 , LYS A:227 , HOH A:2053 , HOH A:2102
BINDING SITE FOR RESIDUE SO4 A 1001
2
AC2
SOFTWARE
GLY B:184 , SER B:185 , HIS B:208 , SER B:221 , ASN B:226 , LYS B:227 , HOH B:2021 , HOH B:2088 , HOH B:2109
BINDING SITE FOR RESIDUE SO4 B 1002
3
AC3
SOFTWARE
GLY A:7 , THR A:9 , GLY A:10 , SER A:11 , ILE A:12 , ALA A:34 , GLY A:35 , LYS A:36 , ASN A:37 , ASP A:56 , ALA A:99 , ILE A:100 , VAL A:101 , ALA A:104 , ALA A:122 , ASN A:123 , ASP A:149 , MSE A:275 , HOH A:2046 , HOH A:2099 , HOH A:2100
BINDING SITE FOR RESIDUE NDP A 2001
4
AC4
SOFTWARE
GLY B:7 , THR B:9 , GLY B:10 , SER B:11 , ILE B:12 , ALA B:34 , GLY B:35 , LYS B:36 , ASN B:37 , ASP B:56 , ALA B:99 , VAL B:101 , ALA B:104 , ALA B:122 , ASN B:123 , LYS B:124 , ASP B:149 , HOH B:2078 , HOH B:2083
BINDING SITE FOR RESIDUE NDP B 2002
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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Exons
(0, 0)
Info
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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
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1jvsa1 (A:301-399)
1b: SCOP_d1jvsb1 (B:301-397)
2a: SCOP_d1jvsa3 (A:126-274)
2b: SCOP_d1jvsb3 (B:126-274)
3a: SCOP_d1jvsa2 (A:0-125,A:275-300)
3b: SCOP_d1jvsb2 (B:0-125,B:275-300)
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(
)
(
)
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(
)
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)
(
)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Left-handed superhelix
(73)
Superfamily
:
1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
(13)
Family
:
1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
(13)
Protein domain
:
1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
(13)
Escherichia coli [TaxId: 562]
(11)
1a
d1jvsa1
A:301-399
1b
d1jvsb1
B:301-397
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
FwdE/GAPDH domain-like
(188)
Superfamily
:
Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
(179)
Family
:
Dihydrodipicolinate reductase-like
(45)
Protein domain
:
1-deoxy-D-xylulose-5-phosphate reductoisomerase
(13)
Escherichia coli [TaxId: 562]
(11)
2a
d1jvsa3
A:126-274
2b
d1jvsb3
B:126-274
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
:
Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
(179)
Protein domain
:
1-deoxy-D-xylulose-5-phosphate reductoisomerase
(13)
Escherichia coli [TaxId: 562]
(11)
3a
d1jvsa2
A:0-125,A:275-300
3b
d1jvsb2
B:0-125,B:275-300
[
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]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1jvsA01 (A:0-149)
1b: CATH_1jvsB01 (B:0-149)
2a: CATH_1jvsA03 (A:311-399)
2b: CATH_1jvsB03 (B:311-397)
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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)
Escherichia coli. Organism_taxid: 562.
(49)
1a
1jvsA01
A:0-149
1b
1jvsB01
B:0-149
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Rna Polymerase Sigma Factor; Chain: A
(22)
Homologous Superfamily
:
[code=1.10.1740.10, no name defined]
(22)
Escherichia coli. Organism_taxid: 562.
(4)
2a
1jvsA03
A:311-399
2b
1jvsB03
B:311-397
[
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Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_DXP_redisom_C_1jvsB01 (B:145-238)
1b: PFAM_DXP_redisom_C_1jvsB02 (B:145-238)
2a: PFAM_DXP_reductoisom_1jvsB03 (B:3-131)
2b: PFAM_DXP_reductoisom_1jvsB04 (B:3-131)
3a: PFAM_DXPR_C_1jvsB05 (B:270-388)
3b: PFAM_DXPR_C_1jvsB06 (B:270-388)
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Clans
(
)
(
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)
(
)
Organisms
(
)
(
)
Clan
:
NADP_Rossmann
(1239)
Family
:
DXP_redisom_C
(19)
Escherichia coli (strain K12)
(10)
1a
DXP_redisom_C-1jvsB01
B:145-238
1b
DXP_redisom_C-1jvsB02
B:145-238
Family
:
DXP_reductoisom
(19)
Escherichia coli (strain K12)
(10)
2a
DXP_reductoisom-1jvsB03
B:3-131
2b
DXP_reductoisom-1jvsB04
B:3-131
Clan
:
no clan defined [family: DXPR_C]
(19)
Family
:
DXPR_C
(19)
Escherichia coli (strain K12)
(10)
3a
DXPR_C-1jvsB05
B:270-388
3b
DXPR_C-1jvsB06
B:270-388
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