SMTL ID : 2nqz.1

Trna-guanine transglycosylase (TGT) mutant in complex with 7-deaza-7-aminomethyl-guanine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.317, C.319, C.322, H.348 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.317, A:C.319, A:C.322, A:H.348 ZN.9: 4 residues within 4Å: Chain B: C.317, C.319, C.322, H.348 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.317, B:C.319, B:C.322, B:H.348

2 x PRF: 7-DEAZA-7-AMINOMETHYL-GUANINE(Non-covalent)

PRF.2: 12 residues within 4Å: Chain A: S.102, G.104, F.105, D.155, V.157, I.200, Q.202, G.228, G.229, L.230, M.259 Ligands: GOL.7 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:M.259 Hydrogen bonds: A:S.102, A:G.104, A:F.105, A:Q.202, A:G.229, A:L.230 Water bridges: A:S.102, A:S.102, A:G.103, A:L.230 Salt bridges: A:D.155 pi-Stacking: A:F.105 PRF.10: 12 residues within 4Å: Chain B: S.102, G.104, F.105, D.155, V.157, I.200, Q.202, G.228, G.229, L.230, M.259 Ligands: GOL.15 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:M.259 Hydrogen bonds: B:S.102, B:G.104, B:F.105, B:Q.202, B:G.229, B:L.230 Water bridges: B:S.102, B:S.102, B:G.103, B:L.230 Salt bridges: B:D.155 pi-Stacking: B:F.105

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: A.18, T.26, G.27, T.28, R.37, T.38, R.361, S.365 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.26, A:G.27, A:T.38 Water bridges: A:R.361 GOL.4: 6 residues within 4Å: Chain A: P.55, E.56, G.93, W.94, D.95, R.96 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.55, A:D.95, A:D.95, A:R.96 Water bridges: A:E.56 GOL.5: 3 residues within 4Å: Chain A: P.251, D.253, K.254 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.254 Water bridges: A:K.254 GOL.6: 5 residues within 4Å: Chain A: H.144, G.147, S.148, Q.191, N.194 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.144 Water bridges: A:G.147, A:D.149, A:Q.191 GOL.7: 7 residues within 4Å: Chain A: V.44, N.69, D.101, Q.106, G.260, D.279 Ligands: PRF.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.69, A:Q.106, A:D.279 Water bridges: A:N.69, A:D.101, A:S.102 GOL.8: 5 residues within 4Å: Chain A: A.304, S.307, H.331, R.335 Chain B: R.81 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.331, B:R.81, B:R.81 Water bridges: A:S.307, A:R.335, A:R.335 GOL.11: 8 residues within 4Å: Chain B: A.18, T.26, G.27, T.28, R.37, T.38, R.361, S.365 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.26, B:G.27, B:T.38 Water bridges: B:R.361 GOL.12: 6 residues within 4Å: Chain B: P.55, E.56, G.93, W.94, D.95, R.96 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:P.55, B:D.95, B:D.95, B:R.96 Water bridges: B:E.56 GOL.13: 3 residues within 4Å: Chain B: P.251, D.253, K.254 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.254 Water bridges: B:K.254 GOL.14: 5 residues within 4Å: Chain B: H.144, G.147, S.148, Q.191, N.194 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.144, B:H.144 Water bridges: B:G.147, B:D.149, B:Q.191 GOL.15: 7 residues within 4Å: Chain B: V.44, N.69, D.101, Q.106, G.260, D.279 Ligands: PRF.10 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.69, B:D.101, B:Q.106, B:D.279 Water bridges: B:N.69, B:D.101, B:S.102 GOL.16: 5 residues within 4Å: Chain A: R.81 Chain B: A.304, S.307, H.331, R.335 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.331, A:R.81, A:R.81 Water bridges: B:S.307, B:R.335, B:R.335

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Biela, I. et al., Investigation of Specificity Determinants in Bacterial tRNA-Guanine Transglycosylase Reveals Queuine, the Substrate of Its Eucaryotic Counterpart, as Inhibitor. Plos One (2013)

Release Date

2007-11-13

Peptides

Queuine tRNA-ribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Queuine tRNA-ribosyltransferase