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1RKD
Biol. Unit 1
Info
Asym.Unit (57 KB)
Biol.Unit 1 (101 KB)
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(1)
Title
:
E. COLI RIBOKINASE COMPLEXED WITH RIBOSE AND ADP
Authors
:
J. A. Sigrell, A. D. Cameron, T. A. Jones, S. L. Mowbray
Date
:
29 Nov 97 (Deposition) - 04 Mar 98 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.84
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Carbohydrate Kinase, Ribose, Nucleotide Binding, Transferase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
J. A. Sigrell, A. D. Cameron, T. A. Jones, S. L. Mowbray
Structure Of Escherichia Coli Ribokinase In Complex With Ribose And Dinucleotide Determined To 1. 8 A Resolution: Insights Into A New Family Of Kinase Structures.
Structure V. 6 183 1998
(for further references see the
PDB file header
)
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Hetero Components
(3, 8)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
2a: PHOSPHATE ION (PO4a)
2b: PHOSPHATE ION (PO4b)
3a: RIBOSE (RIBa)
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Label:
No.
Name
Count
Type
Full Name
1
ADP
2
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
PO4
4
Ligand/Ion
PHOSPHATE ION
3
RIB
2
Ligand/Ion
RIBOSE
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Sites
(10, 10)
Info
All Sites
01: AB1 (UNKNOWN)
02: AB2 (UNKNOWN)
03: AB3 (UNKNOWN)
04: AC1 (SOFTWARE)
05: AC2 (SOFTWARE)
06: AC3 (SOFTWARE)
07: AC4 (SOFTWARE)
08: RB1 (UNKNOWN)
09: RB2 (UNKNOWN)
10: RB3 (UNKNOWN)
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No.
Name
Evidence
Residues
Description
01
AB1
UNKNOWN
ASN A:187 , THR A:223 , GLY A:225 , ALA A:280
RESIDUES MAKING DIRECT HYDROGEN BONDS WITH ADP.
02
AB2
UNKNOWN
ASN A:166 , ASN A:187 , GLU A:190 , THR A:223 , PHE A:243 , VAL A:245 , ALA A:280
RESIDUES MAKING WATER-MEDIATED HYDROGEN BONDS WITH ADP.
03
AB3
UNKNOWN
GLY A:225 , VAL A:245 , ALA A:253 , ALA A:282 , VAL A:286
RESIDUES WITHIN VAN DER WAALS DISTANCE OF ADP.
04
AC1
SOFTWARE
ASN A:14 , ASP A:16 , GLY A:41 , GLY A:42 , LYS A:43 , ASN A:46 , ALA A:98 , GLU A:143 , ASP A:255 , HOH A:376
BINDING SITE FOR RESIDUE RIB A 311
05
AC2
SOFTWARE
GLU A:29 , THR A:30 , PRO A:169 , ALA A:170 , ASN A:187 , GLU A:190 , HOH A:430
BINDING SITE FOR RESIDUE PO4 A 312
06
AC3
SOFTWARE
HIS A:17 , HOH A:323 , HOH A:379 , HOH A:494
BINDING SITE FOR RESIDUE PO4 A 313
07
AC4
SOFTWARE
ASN A:187 , THR A:223 , GLY A:225 , GLY A:228 , PHE A:243 , ALA A:253 , GLY A:254 , HIS A:279 , ALA A:282 , HOH A:372 , HOH A:393 , HOH A:405 , HOH A:429 , HOH A:492
BINDING SITE FOR RESIDUE ADP A 310
08
RB1
UNKNOWN
ASN A:14 , ASP A:16 , GLY A:42 , LYS A:43 , ASN A:46 , GLU A:143 , ASP A:255
RESIDUES MAKING DIRECT HYDROGEN BONDS WITH RIBOSE.
09
RB2
UNKNOWN
ALA A:252 , GLY A:254 , ASP A:255
RESIDUES MAKING WATER-MEDIATED HYDROGEN BONDS WITH RIBOSE.
10
RB3
UNKNOWN
ALA A:98 , ILE A:100 , ILE A:110 , ILE A:112 , ILE A:251
RESIDUES WITHIN VAN DER WAALS DISTANCE OF RIBOSE.
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PFKB_KINASES_2 (A:249-262)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PFKB_KINASES_2
PS00584
pfkB family of carbohydrate kinases signature 2.
RBSK_ECOLI
249-262
2
A:249-262
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Exons
(0, 0)
Info
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1rkda_ (A:)
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Protein Domains
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)
(
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Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribokinase-like
(226)
Superfamily
:
Ribokinase-like
(189)
Family
:
Ribokinase-like
(36)
Protein domain
:
Ribokinase
(7)
Escherichia coli [TaxId: 562]
(5)
1a
d1rkda_
A:
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CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1rkdA00 (A:4-309)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
(109)
Homologous Superfamily
:
[code=3.40.1190.20, no name defined]
(73)
Escherichia coli k12. Organism_taxid: 83333. Strain: k12. Cell_line: s2.
(1)
1a
1rkdA00
A:4-309
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Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_PfkB_1rkdA01 (A:4-298)
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Clans
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Organisms
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)
Clan
:
Ribokinase
(55)
Family
:
PfkB
(39)
Escherichia coli (strain K12)
(4)
1a
PfkB-1rkdA01
A:4-298
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