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1LK7
Asym. Unit
Info
Asym.Unit (158 KB)
Biol.Unit 1 (153 KB)
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(1)
Title
:
STRUCTURE OF D-RIBOSE-5-PHOSPHATE ISOMERASE FROM IN COMPLEX WITH PHOSPHO-ERYTHRONIC ACID
Authors
:
K. Ishikawa, I. Matsui, F. Payan, C. Cambillau, H. Ishida, Y. Kawarabayasi, H. Kikuchi, A. Roussel
Date
:
24 Apr 02 (Deposition) - 03 Jul 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Alpha/Beta Structure, Isomerase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Ishikawa, I. Matsui, F. Payan, C. Cambillau, H. Ishida, Y. Kawarabayasi, H. Kikuchi, A. Roussel
A Hyperthermostable D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii Characterization And Three-Dimensional Structure
Structure V. 10 877 2002
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 16)
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)
2a: D-4-PHOSPHOERYTHRONIC ACID (DERa)
2b: D-4-PHOSPHOERYTHRONIC ACID (DERb)
2c: D-4-PHOSPHOERYTHRONIC ACID (DERc)
2d: D-4-PHOSPHOERYTHRONIC ACID (DERd)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
10
Ligand/Ion
CHLORIDE ION
2
DER
4
Ligand/Ion
D-4-PHOSPHOERYTHRONIC ACID
3
NA
2
Ligand/Ion
SODIUM ION
[
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Sites
(16, 16)
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)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:99 , GLY A:101 , ALA A:102 , ALA A:103 , GLU A:107 , DER A:1001
BINDING SITE FOR RESIDUE CL A 2001
02
AC2
SOFTWARE
GLY B:99 , GLY B:101 , ALA B:102 , ALA B:103 , GLU B:107 , DER B:1002
BINDING SITE FOR RESIDUE CL B 2002
03
AC3
SOFTWARE
GLY C:99 , GLY C:101 , ALA C:102 , ALA C:103 , GLU C:107 , DER C:1003
BINDING SITE FOR RESIDUE CL C 2003
04
AC4
SOFTWARE
GLY D:99 , GLY D:101 , ALA D:102 , ALA D:103 , GLU D:107 , DER D:1004
BINDING SITE FOR RESIDUE CL D 2004
05
AC5
SOFTWARE
SER A:57 , TYR A:58 , GLN A:59 , ASP A:174 , LYS C:167 , ASP C:168 , GLY C:169
BINDING SITE FOR RESIDUE CL A 2005
06
AC6
SOFTWARE
SER B:57 , TYR B:58 , GLN B:59 , ASP B:174 , HOH B:2036 , LYS D:167 , ASP D:168 , GLY D:169
BINDING SITE FOR RESIDUE CL B 2006
07
AC7
SOFTWARE
LYS A:167 , ASP A:168 , GLY A:169 , SER C:57 , TYR C:58 , GLN C:59 , ASP C:174
BINDING SITE FOR RESIDUE CL C 2007
08
AC8
SOFTWARE
LYS B:167 , ASP B:168 , SER D:57 , TYR D:58 , GLN D:59 , ASP D:174
BINDING SITE FOR RESIDUE CL D 2008
09
AC9
SOFTWARE
VAL A:165 , ASN A:166 , VAL C:165 , ASN C:166
BINDING SITE FOR RESIDUE CL A 2009
10
BC1
SOFTWARE
VAL B:165 , ASN B:166 , VAL D:165 , ASN D:166
BINDING SITE FOR RESIDUE CL B 2010
11
BC2
SOFTWARE
ASN A:175 , HOH A:2019 , HOH A:2049 , HOH A:2050 , ASN B:175 , HOH B:2026
BINDING SITE FOR RESIDUE NA A 2011
12
BC3
SOFTWARE
ASN C:175 , HOH C:2051 , HOH C:2052 , ASN D:175 , HOH D:2039 , HOH D:2040
BINDING SITE FOR RESIDUE NA C 2012
13
BC4
SOFTWARE
THR A:28 , SER A:30 , THR A:31 , ASP A:85 , GLY A:86 , ALA A:87 , ASP A:88 , LYS A:98 , GLY A:99 , ARG A:100 , GLY A:101 , GLU A:107 , LYS A:125 , CL A:2001 , HOH A:2052 , HOH A:2053 , HOH A:2098
BINDING SITE FOR RESIDUE DER A 1001
14
BC5
SOFTWARE
THR B:28 , SER B:30 , THR B:31 , ASP B:85 , GLY B:86 , ALA B:87 , ASP B:88 , LYS B:98 , GLY B:99 , GLY B:101 , GLU B:107 , LYS B:125 , CL B:2002 , HOH B:2031 , HOH B:2038 , HOH D:2082
BINDING SITE FOR RESIDUE DER B 1002
15
BC6
SOFTWARE
THR C:28 , GLY C:29 , SER C:30 , THR C:31 , ASP C:85 , GLY C:86 , ALA C:87 , ASP C:88 , LYS C:98 , GLY C:99 , ARG C:100 , GLY C:101 , GLU C:107 , LYS C:125 , CL C:2003 , HOH C:2020 , HOH C:2055 , HOH C:2059 , HOH C:2074 , HOH C:2100
BINDING SITE FOR RESIDUE DER C 1003
16
BC7
SOFTWARE
THR D:28 , SER D:30 , THR D:31 , ASP D:85 , GLY D:86 , ALA D:87 , ASP D:88 , LYS D:98 , GLY D:99 , GLY D:101 , GLU D:107 , LYS D:125 , CL D:2004 , HOH D:2035 , HOH D:2054 , HOH D:2055 , HOH D:2105
BINDING SITE FOR RESIDUE DER D 1004
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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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
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1lk7a2 (A:131-210)
1b: SCOP_d1lk7b2 (B:131-210)
1c: SCOP_d1lk7c2 (C:131-210)
1d: SCOP_d1lk7d2 (D:131-210)
2a: SCOP_d1lk7a1 (A:1-130,A:211-229)
2b: SCOP_d1lk7b1 (B:1-130,B:211-229)
2c: SCOP_d1lk7c1 (C:1-130,C:211-229)
2d: SCOP_d1lk7d1 (D:1-130,D:211-229)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
D-ribose-5-phosphate isomerase (RpiA), lid domain
(9)
Family
:
D-ribose-5-phosphate isomerase (RpiA), lid domain
(9)
Protein domain
:
D-ribose-5-phosphate isomerase (RpiA), lid domain
(9)
Pyrococcus horikoshii [TaxId: 53953]
(2)
1a
d1lk7a2
A:131-210
1b
d1lk7b2
B:131-210
1c
d1lk7c2
C:131-210
1d
d1lk7d2
D:131-210
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NagB/RpiA/CoA transferase-like
(94)
Superfamily
:
NagB/RpiA/CoA transferase-like
(94)
Family
:
D-ribose-5-phosphate isomerase (RpiA), catalytic domain
(9)
Protein domain
:
D-ribose-5-phosphate isomerase (RpiA), catalytic domain
(9)
Pyrococcus horikoshii [TaxId: 53953]
(2)
2a
d1lk7a1
A:1-130,A:211-229
2b
d1lk7b1
B:1-130,B:211-229
2c
d1lk7c1
C:1-130,C:211-229
2d
d1lk7d1
D:1-130,D:211-229
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1lk7A02 (A:129-207)
1b: CATH_1lk7B02 (B:129-207)
1c: CATH_1lk7C02 (C:129-207)
1d: CATH_1lk7D02 (D:129-207)
2a: CATH_1lk7A01 (A:1-128,A:208-229)
2b: CATH_1lk7B01 (B:1-128,B:208-229)
2c: CATH_1lk7C01 (C:1-128,C:208-229)
2d: CATH_1lk7D01 (D:1-128,D:208-229)
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Classes
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)
(
)
Architectures
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)
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)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.260, no name defined]
(34)
Pyrococcus horikoshii. Organism_taxid: 53953.
(2)
1a
1lk7A02
A:129-207
1b
1lk7B02
B:129-207
1c
1lk7C02
C:129-207
1d
1lk7D02
D:129-207
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.1360, no name defined]
(40)
Pyrococcus horikoshii. Organism_taxid: 53953.
(2)
2a
1lk7A01
A:1-128,A:208-229
2b
1lk7B01
B:1-128,B:208-229
2c
1lk7C01
C:1-128,C:208-229
2d
1lk7D01
D:1-128,D:208-229
[
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]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Rib_5_P_isom_A_1lk7D01 (D:51-225)
1b: PFAM_Rib_5_P_isom_A_1lk7D02 (D:51-225)
1c: PFAM_Rib_5_P_isom_A_1lk7D03 (D:51-225)
1d: PFAM_Rib_5_P_isom_A_1lk7D04 (D:51-225)
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Clans
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Families
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(
)
Organisms
(
)
(
)
Clan
:
ISOCOT_Fold
(53)
Family
:
Rib_5-P_isom_A
(10)
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
(2)
1a
Rib_5-P_isom_A-1lk7D01
D:51-225
1b
Rib_5-P_isom_A-1lk7D02
D:51-225
1c
Rib_5-P_isom_A-1lk7D03
D:51-225
1d
Rib_5-P_isom_A-1lk7D04
D:51-225
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