SMTL ID : 2vbv.1 (1 other biounit)

Riboflavin kinase Mj0056 from Methanocaldococcus jannaschii in complex with CDP and FMN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 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, 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, FMN.5 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.14, A:G.16, A:G.16, A:G.18, A:R.19, A:T.43, A:N.45, A:A.110, A:M.112, A:L.114, A:R.115, 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 Ligands: CDP.1, FMN.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:T.43, A:T.43, FMN.5

1 x IOD: IODIDE ION(Non-functional Binders)

IOD.3: 2 residues within 4Å: Chain A: Y.20, N.68 Ligand excluded by PLIP

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain A: S.13, D.122 Ligand excluded by PLIP

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.5: 20 residues within 4Å: Chain A: G.16, E.17, G.18, F.21, Y.27, F.31, T.43, N.45, F.72, F.73, V.75, V.94, P.96, K.98, T.99, Y.100, H.101, E.107 Ligands: CDP.1, MG.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.21, A:F.31, A:T.43, A:V.75, A:V.94, A:P.96 Hydrogen bonds: A:L.15, A:E.17, A:G.18, A:T.43, A:N.45, A:N.45, A:F.73, A:T.99, A:Y.100, A:Y.100, A:E.107 Water bridges: A:K.98 pi-Stacking: A:F.21

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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