SMTL ID : 4kqi.1

Crystal structure of CobT E317A complexed with its reaction products

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

2 x RBZ: ALPHA-RIBAZOLE-5'-PHOSPHATE(Non-covalent)

RBZ.1: 18 residues within 4Å: Chain A: A.78, S.80, V.84, Q.88, E.174, L.175, G.176, M.177, A.178, N.179, T.180, G.202, A.203, L.315, G.316, A.317 Chain B: P.32 Ligands: NIO.3 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.84, B:P.32 Hydrogen bonds: A:E.174, A:G.176, A:G.176, A:A.178, A:T.180, A:T.180, A:A.203, A:A.317 Water bridges: A:V.77, A:V.79, A:V.79, A:Q.88, A:T.180, A:T.181 Salt bridges: A:K.213 RBZ.4: 18 residues within 4Å: Chain A: P.32 Chain B: A.78, S.80, V.84, Q.88, E.174, L.175, G.176, M.177, A.178, N.179, T.180, G.202, A.203, L.315, G.316, A.317 Ligands: NIO.6 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.84, A:P.32 Hydrogen bonds: B:E.174, B:G.176, B:G.176, B:A.178, B:T.180, B:A.203, B:A.317 Water bridges: B:V.77, B:V.79, B:V.79, B:Q.88, B:T.180, B:T.181 Salt bridges: B:K.213

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: C.100, A.108, K.109, V.110 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.100, A:A.104, A:V.110, A:V.110 EDO.5: 4 residues within 4Å: Chain B: C.100, A.108, K.109, V.110 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:C.100, B:A.104, B:V.110, B:V.110

2 x NIO: NICOTINIC ACID(Non-covalent)

NIO.3: 11 residues within 4Å: Chain A: T.180, G.202, G.264, F.265, L.266, S.291, E.293, R.314, L.315, G.316 Ligands: RBZ.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:T.180, A:L.266, A:R.314 Hydrogen bonds: A:F.265, A:S.291 Water bridges: A:D.263, A:D.263, A:G.264, A:G.316, A:G.316 NIO.6: 11 residues within 4Å: Chain B: T.180, G.202, G.264, F.265, L.266, S.291, E.293, R.314, L.315, G.316 Ligands: RBZ.4 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:T.180, B:L.266, B:R.314 Hydrogen bonds: B:F.265, B:S.291 Water bridges: B:D.263, B:G.264, B:G.316, B:G.316

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chan, C.H. et al., Dissecting cobamide diversity through structural and functional analyses of the base-activating CobT enzyme of Salmonella enterica. Biochim.Biophys.Acta (2014)

Release Date

2014-03-12

Peptides

Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase

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