SMTL ID : 5a89.1 (1 other biounit)

Crystal structure of the riboflavin kinase module of FAD synthetase from Corynebacterium ammoniagenes in complex with FMN and ADP(P 21 21 21)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 26 residues within 4Å: Chain A: G.14, A.15, G.16, R.17, G.18, L.22, T.26, N.28, V.42, A.69, S.71, N.75, P.76, T.77, F.78, E.86, F.88, R.110, M.112, E.113, F.115, L.121, M.125, D.128 Ligands: MG.2, ADP.4 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:T.26, A:V.42, A:V.42, A:A.69, A:F.88 Hydrogen bonds: A:A.15, A:G.16, A:R.17, A:R.17, A:G.18, A:T.26, A:N.28, A:T.77, A:T.77, A:R.110, A:R.110, A:E.113, A:E.113 Water bridges: A:Y.30 Salt bridges: A:R.17

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: T.26, N.28, E.86 Ligands: FMN.1, ADP.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:T.26, A:T.26, FMN.1

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: H.4, D.139, H.143 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.4, A:D.139, A:H.143, H2O.1

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

ADP.4: 23 residues within 4Å: Chain A: V.11, R.13, G.14, A.15, G.16, R.17, G.18, G.19, P.25, T.26, A.27, N.28, S.87, F.88, V.89, R.92, D.93, A.94, D.95, L.96, Y.97 Ligands: FMN.1, MG.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.14, A:G.16, A:R.17, A:G.18, A:G.19, A:T.26, A:V.89, A:V.89, A:A.94, A:L.96, A:Y.97, A:Y.97 Water bridges: A:K.20, A:T.26, A:N.28, A:R.92

1 x ACY: ACETIC ACID(Non-functional Binders)

ACY.5: 1 residues within 4Å: Chain A: R.92 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.59, A:N.59, A:N.59 Salt bridges: A:R.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Herguedas, B. et al., Structural Insights Into the Synthesis of Fmn in Prokaryotic Organisms. Acta Crystallogr.,Sect.D (2015)

Release Date

2015-12-09

Peptides

RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF

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