SMTL ID : 3uxj.1 (1 other biounit)

Crystal Structure of 7-cyano-7-deazaguanine reductase, QueF from Vibrio cholerae complexed with NADP and PreQ0

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

2 x PRF: 7-DEAZA-7-AMINOMETHYL-GUANINE(Covalent)

PRF.1: 16 residues within 4Å: Chain A: W.65, L.95, I.96, E.97, S.98, C.197, L.198, T.200, D.204, E.234, F.235, H.236, E.237, L.265, I.270 Ligands: NAP.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:I.96, A:E.97, A:S.98, A:H.236, A:H.236 Salt bridges: A:E.237 pi-Stacking: A:F.235, A:F.235 pi-Cation interactions: A:F.235 PRF.5: 14 residues within 4Å: Chain B: W.65, L.95, I.96, E.97, S.98, C.197, I.199, D.204, E.234, F.235, H.236, E.237, L.265, I.270 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:I.96, B:E.97, B:E.97, B:S.98, B:D.204, B:H.236 Water bridges: B:H.236 Salt bridges: B:E.237 pi-Stacking: B:F.235, B:F.235 pi-Cation interactions: B:F.235

1 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.2: 12 residues within 4Å: Chain A: S.98, K.99, K.102, T.200, L.265, G.266 Chain B: K.99, K.102, Q.202, L.265, G.266 Ligands: PRF.1 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.99, A:T.200, A:G.266, B:G.266 Water bridges: A:K.99, A:K.99, A:G.267, A:G.267, B:G.267 Salt bridges: A:K.99

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

EDO.3: 5 residues within 4Å: Chain A: A.211, Y.212, H.213, S.255, Q.278 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.255, A:S.255 Water bridges: A:L.256 EDO.4: 4 residues within 4Å: Chain A: C.157, I.158, Q.161, R.219 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.157, A:R.219 Water bridges: A:Q.161 EDO.6: 6 residues within 4Å: Chain B: E.164, I.165, A.166, N.167, L.174, R.224 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.166, B:N.167, B:R.224, B:R.224 EDO.7: 5 residues within 4Å: Chain A: N.143 Chain B: T.152, C.157, H.189, H.191 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.191 Water bridges: B:T.152, B:G.155, B:C.157 EDO.8: 5 residues within 4Å: Chain B: Q.154, E.209, T.257, Y.259, H.283 No protein-ligand interaction detected (PLIP) EDO.9: 5 residues within 4Å: Chain B: G.181, E.182, K.216, M.217, N.218 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.181, B:E.182, B:K.216 Water bridges: B:N.218, B:N.218 EDO.10: 5 residues within 4Å: Chain B: Y.145, E.148, P.149, Q.285, R.286 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.286, B:R.286

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of 7-cyano-7-deazaguanine reductase, QueF from Vibrio cholerae complexed with NADP and PreQ0. To be Published (2012)

Release Date

2012-01-04

Peptides

NADPH-dependent 7-cyano-7-deazaguanine reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NADPH-dependent 7-cyano-7-deazaguanine reductase

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