SMTL ID : 5trd.1

Structure of RbkR (Riboflavin Kinase) from Thermoplasma acidophilum determined in complex with CTP and its cognate DNA operator

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.1: 18 residues within 4Å: Chain A: S.103, G.104, M.105, G.106, E.107, G.108, R.109, Y.130, G.132, T.133, L.134, N.135, S.200, K.202, Y.203, L.204, R.205 Ligands: NA.2 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:Y.130 Hydrogen bonds: A:G.104, A:M.105, A:G.106, A:E.107, A:G.108, A:R.109, A:Y.130, A:T.133, A:N.135, A:N.135, A:S.200, A:K.202, A:L.204, A:R.205, A:R.205, A:R.205 Water bridges: A:T.102, A:R.109, A:T.133, A:T.133, A:N.135, A:Y.203 CTP.3: 18 residues within 4Å: Chain B: S.103, G.104, M.105, G.106, E.107, G.108, R.109, Y.130, G.132, T.133, L.134, N.135, S.200, K.202, Y.203, L.204, R.205 Ligands: NA.4 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.130 Hydrogen bonds: B:G.104, B:M.105, B:G.106, B:E.107, B:G.108, B:R.109, B:T.133, B:T.133, B:N.135, B:S.200, B:K.202, B:L.204, B:R.205, B:R.205, B:R.205

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 4 residues within 4Å: Chain A: T.133, N.135, E.197 Ligands: CTP.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.133, A:N.135, A:E.197 Water bridges: A:N.135 NA.4: 4 residues within 4Å: Chain B: T.133, N.135, E.197 Ligands: CTP.3 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.133, B:T.133, B:N.135, B:E.197 Water bridges: B:G.108, B:N.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vetting, M.W. et al., Structure of RbkR (Riboflavin Kinase) from Thermoplasma acidophilum determined in complex with CTP and its cognate DNA operator. To be published

Release Date

2016-11-23

Peptides

Riboflavin kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Riboflavin kinase

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