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1M5W
Asym. Unit
Info
Asym.Unit (319 KB)
Biol.Unit 1 (314 KB)
Biol.Unit 2 (83 KB)
Biol.Unit 3 (83 KB)
Biol.Unit 4 (82 KB)
Biol.Unit 5 (82 KB)
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(1)
Title
:
1.96 A CRYSTAL STRUCTURE OF PYRIDOXINE 5'-PHOSPHATE SYNTHASE IN COMPLEX WITH 1-DEOXY-D-XYLULOSE PHOSPHATE
Authors
:
J. I. Yeh, S. Du, E. Pohl, D. E. Cane
Date
:
10 Jul 02 (Deposition) - 15 Jul 03 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.96
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D,E,F,G,H (1x)
Biol. Unit 2: C,F (1x)
Biol. Unit 3: A,E (1x)
Biol. Unit 4: B,G (1x)
Biol. Unit 5: D,H (1x)
Keywords
:
Tim Barrel, Protein-Substrate Complex, Multi-Binding States, Biosynthetic Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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Reference
:
J. I. Yeh, S. Du, E. Pohl, D. E. Cane
Multistate Binding In Pyridoxine 5'-Phosphate Synthase: 1. 9 A Crystal Structure In Complex With 1-Deoxy-D-Xylulose Phosphate
Biochemistry V. 41 11649 2002
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: 1-DEOXY-D-XYLULOSE-5-PHOSPHATE (DXPa)
1b: 1-DEOXY-D-XYLULOSE-5-PHOSPHATE (DXPb)
1c: 1-DEOXY-D-XYLULOSE-5-PHOSPHATE (DXPc)
1d: 1-DEOXY-D-XYLULOSE-5-PHOSPHATE (DXPd)
1e: 1-DEOXY-D-XYLULOSE-5-PHOSPHATE (DXPe)
1f: 1-DEOXY-D-XYLULOSE-5-PHOSPHATE (DXPf)
2a: PHOSPHATE ION (PO4a)
2b: PHOSPHATE ION (PO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DXP
6
Ligand/Ion
1-DEOXY-D-XYLULOSE-5-PHOSPHATE
2
PO4
2
Ligand/Ion
PHOSPHATE ION
[
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:9 , ASP A:11 , HIS A:12 , HIS A:45 , ARG A:47 , GLU A:72 , THR A:102 , THR A:103 , GLU A:153 , HIS A:193 , PO4 A:1101 , HOH A:1146 , HOH A:1158 , ARG E:20 , HOH E:1020
BINDING SITE FOR RESIDUE DXP A 1001
2
AC2
SOFTWARE
ASN B:9 , ASP B:11 , HIS B:45 , HIS B:52 , GLU B:72 , HIS B:193 , GLY B:215 , HIS B:216 , HOH B:1071 , HOH G:1071
BINDING SITE FOR RESIDUE DXP B 1002
3
AC3
SOFTWARE
ASP C:11 , HIS C:12 , HIS C:45 , HIS C:52 , GLU C:72 , THR C:102 , THR C:103 , HIS C:193 , PO4 C:1103 , HOH C:1145 , HOH C:1194 , HOH C:1195 , HOH C:1197 , ARG F:20 , HOH F:1099
BINDING SITE FOR RESIDUE DXP C 1003
4
AC4
SOFTWARE
ARG A:20 , ASP E:11 , HIS E:45 , HIS E:52 , GLU E:72 , LYS E:97 , HIS E:193 , GLY E:215 , HIS E:216 , HOH E:1058
BINDING SITE FOR RESIDUE DXP E 1005
5
AC5
SOFTWARE
ARG C:20 , ASN F:9 , ASP F:11 , HIS F:45 , ARG F:47 , HIS F:52 , GLU F:72 , HIS F:193 , GLY F:215 , HIS F:216 , HOH F:1043
BINDING SITE FOR RESIDUE DXP F 1006
6
AC6
SOFTWARE
ARG B:20 , ASN G:9 , ASP G:11 , HIS G:45 , ARG G:51 , HIS G:52 , GLU G:72 , HIS G:193 , GLY G:194 , GLY G:215 , HIS G:216 , HOH G:1106 , HOH G:1107
BINDING SITE FOR RESIDUE DXP G 1007
7
AC7
SOFTWARE
HIS A:193 , GLY A:194 , ILE A:214 , GLY A:215 , HIS A:216 , DXP A:1001 , HOH A:1120 , HOH A:1139 , HOH A:1146 , ARG E:20
BINDING SITE FOR RESIDUE PO4 A 1101
8
AC8
SOFTWARE
HIS C:193 , GLY C:194 , ILE C:214 , GLY C:215 , HIS C:216 , DXP C:1003 , HOH C:1118 , HOH C:1145 , HOH C:1194 , ARG F:20
BINDING SITE FOR RESIDUE PO4 C 1103
[
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SAPs(SNPs)/Variants
(1, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_PDXJ_ECOLI_001 (G194S, chain A/B/C/D/E/F/G/H, )
View:
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Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_PDXJ_ECOLI_001
*
G
194
S
PDXJ_ECOLI
---
---
A/B/C/D/E/F/G/H
G
194
S
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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
(1, 8)
Info
All SCOP Domains
1a: SCOP_d1m5wa_ (A:)
1b: SCOP_d1m5wb_ (B:)
1c: SCOP_d1m5wc_ (C:)
1d: SCOP_d1m5wd_ (D:)
1e: SCOP_d1m5we_ (E:)
1f: SCOP_d1m5wf_ (F:)
1g: SCOP_d1m5wg_ (G:)
1h: SCOP_d1m5wh_ (H:)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Pyridoxine 5'-phosphate synthase
(11)
Family
:
Pyridoxine 5'-phosphate synthase
(8)
Protein domain
:
Pyridoxine 5'-phosphate synthase
(7)
Escherichia coli [TaxId: 562]
(7)
1a
d1m5wa_
A:
1b
d1m5wb_
B:
1c
d1m5wc_
C:
1d
d1m5wd_
D:
1e
d1m5we_
E:
1f
d1m5wf_
F:
1g
d1m5wg_
G:
1h
d1m5wh_
H:
[
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CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1m5wA00 (A:2-243)
1b: CATH_1m5wB00 (B:2-243)
1c: CATH_1m5wC00 (C:2-243)
1d: CATH_1m5wD00 (D:2-243)
1e: CATH_1m5wE00 (E:2-243)
1f: CATH_1m5wF00 (F:2-243)
1g: CATH_1m5wG00 (G:2-243)
1h: CATH_1m5wH00 (H:2-243)
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Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Aldolase class I
(887)
Escherichia coli. Organism_taxid: 562.
(43)
1a
1m5wA00
A:2-243
1b
1m5wB00
B:2-243
1c
1m5wC00
C:2-243
1d
1m5wD00
D:2-243
1e
1m5wE00
E:2-243
1f
1m5wF00
F:2-243
1g
1m5wG00
G:2-243
1h
1m5wH00
H:2-243
[
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Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_PdxJ_1m5wH01 (H:4-240)
1b: PFAM_PdxJ_1m5wH02 (H:4-240)
1c: PFAM_PdxJ_1m5wH03 (H:4-240)
1d: PFAM_PdxJ_1m5wH04 (H:4-240)
1e: PFAM_PdxJ_1m5wH05 (H:4-240)
1f: PFAM_PdxJ_1m5wH06 (H:4-240)
1g: PFAM_PdxJ_1m5wH07 (H:4-240)
1h: PFAM_PdxJ_1m5wH08 (H:4-240)
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)
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(
)
(
)
Clan
:
TIM_barrel
(694)
Family
:
PdxJ
(3)
Escherichia coli (strain K12)
(1)
1a
PdxJ-1m5wH01
H:4-240
1b
PdxJ-1m5wH02
H:4-240
1c
PdxJ-1m5wH03
H:4-240
1d
PdxJ-1m5wH04
H:4-240
1e
PdxJ-1m5wH05
H:4-240
1f
PdxJ-1m5wH06
H:4-240
1g
PdxJ-1m5wH07
H:4-240
1h
PdxJ-1m5wH08
H:4-240
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