SMTL ID : 1rkd.1

E. COLI RIBOKINASE COMPLEXED WITH RIBOSE AND ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-dimer

Ligands

2 x RIB: alpha-D-ribofuranose(Non-covalent)

RIB.1: 11 residues within 4Å: Chain A: N.14, D.16, G.41, G.42, K.43, N.46, A.98, I.100, I.110, E.143, D.255 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.14, A:D.16, A:G.42, A:K.43, A:K.43, A:N.46, A:E.143 Water bridges: A:A.252, A:A.252, A:D.255 Salt bridges: A:K.43 RIB.5: 11 residues within 4Å: Chain B: N.14, D.16, G.41, G.42, K.43, N.46, A.98, I.100, I.110, E.143, D.255 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:N.14, B:D.16, B:G.42, B:K.43, B:K.43, B:N.46, B:E.143 Water bridges: B:A.252, B:A.252, B:D.255 Salt bridges: B:K.43

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 8 residues within 4Å: Chain A: P.169, A.170, N.187, T.189, E.190 Chain B: G.28, E.29, T.30 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:T.30, B:T.30, A:A.170, A:N.187, A:N.187, A:E.190 PO4.3: 4 residues within 4Å: Chain A: H.17, V.38 Chain B: H.17 Ligands: PO4.7 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:H.17, B:H.17 PO4.6: 8 residues within 4Å: Chain A: G.28, E.29, T.30 Chain B: P.169, A.170, N.187, T.189, E.190 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:A.170, B:N.187, B:N.187, A:T.30, A:T.30, A:T.30 PO4.7: 4 residues within 4Å: Chain A: H.17 Chain B: H.17, V.38 Ligands: PO4.3 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:H.17, B:H.17

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.4: 13 residues within 4Å: Chain A: N.187, T.223, L.224, G.225, S.226, G.228, F.243, V.245, A.253, G.254, F.257, H.279, A.282 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.187, A:T.223, A:G.225, A:G.254, A:H.279 Water bridges: A:N.166, A:T.223, A:V.245, A:V.245, A:V.245, A:A.252, A:D.255 ADP.8: 13 residues within 4Å: Chain B: N.187, T.223, L.224, G.225, S.226, G.228, F.243, V.245, A.253, G.254, F.257, H.279, A.282 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:N.187, B:T.223, B:G.225, B:G.254, B:H.279 Water bridges: B:N.166, B:T.223, B:V.245, B:V.245, B:V.245, B:A.252, B:D.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sigrell, J.A. et al., 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 (1998)

Release Date

1998-03-04

Peptides

RIBOKINASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

RIBOKINASE

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