SMTL ID : 2vbu.1

Riboflavin kinase Mj0056 from Methanocaldococcus jannaschii in complex with CDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x CDP: CYTIDINE-5'-DIPHOSPHATE(Non-covalent)

CDP.1: 18 residues within 4Å: Chain A: S.13, G.14, L.15, G.16, E.17, G.18, R.19, Y.40, G.42, T.43, L.44, N.45, A.110, M.112, K.113, L.114, R.115 Ligands: MG.2 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:G.14, A:G.14, A:G.16, A:G.16, A:E.17, A:G.18, A:R.19, A:T.43, A:T.43, A:A.110, A:M.112, A:L.114, A:R.115, A:R.115 Water bridges: A:S.13, A:T.43, A:N.45, A:N.45, A:N.45, A:N.45, A:R.115 pi-Stacking: A:Y.40

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.43, N.45, E.107 Ligands: CDP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.43, A:T.43, H2O.6

3 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.3: 2 residues within 4Å: Chain A: Y.20, F.21 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.20, A:Y.20, A:Y.20, A:F.21 MRD.4: 7 residues within 4Å: Chain A: F.21, L.22, Y.27, T.43, V.94, P.96, E.107 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.21, A:F.21, A:L.22, A:T.43 Hydrogen bonds: A:E.107 MRD.5: 6 residues within 4Å: Chain A: L.4, P.79, I.80, K.81, L.129, K.131 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.4, A:K.131 Water bridges: A:P.79, A:K.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ammelburg, M. et al., A Ctp-Dependent Archaeal Riboflavin Kinase Forms a Bridge in the Evolution of Cradle-Loop Barrels. Structure (2007)

Release Date

2007-11-20

Peptides

RIBOFLAVIN KINASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RIBOFLAVIN KINASE

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