SMTL ID : 4m4s.1

Gamma subunit of the translation initiation factor 2 from Sulfolobus solfataricus in complex with GDP and formate ion mimic aIF2gamma*GDP*Pi complex (a formate ion substitutes for Pi)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

29 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 5 residues within 4Å: Chain A: M.45, T.46, P.95, G.96, H.97 Ligand excluded by PLIP FMT.2: 4 residues within 4Å: Chain A: S.268, Y.269, V.325, W.327 Ligand excluded by PLIP FMT.3: 4 residues within 4Å: Chain A: R.219, S.220, T.306, K.307 Ligand excluded by PLIP FMT.4: 6 residues within 4Å: Chain A: S.314, I.315, V.361, S.364, V.386, A.387 Ligand excluded by PLIP FMT.5: 3 residues within 4Å: Chain A: K.36, H.37, S.38 Ligand excluded by PLIP FMT.6: 3 residues within 4Å: Chain A: A.342, K.343, E.344 Ligand excluded by PLIP FMT.7: 3 residues within 4Å: Chain A: N.121, K.150 Ligands: GDP.30 Ligand excluded by PLIP FMT.8: 5 residues within 4Å: Chain A: T.365, T.366, L.367, R.383, R.384 Ligand excluded by PLIP FMT.9: 4 residues within 4Å: Chain A: K.254, F.273, A.319, D.320 Ligand excluded by PLIP FMT.10: 6 residues within 4Å: Chain A: S.35, K.36, E.39, E.40, T.46, N.224 Ligand excluded by PLIP FMT.11: 3 residues within 4Å: Chain A: H.37, E.40, L.41 Ligand excluded by PLIP FMT.12: 4 residues within 4Å: Chain A: E.53, N.55, R.88 Ligands: FMT.13 Ligand excluded by PLIP FMT.13: 3 residues within 4Å: Chain A: N.55, R.88 Ligands: FMT.12 Ligand excluded by PLIP FMT.14: 2 residues within 4Å: Chain A: K.64, Y.68 Ligand excluded by PLIP FMT.15: 3 residues within 4Å: Chain A: K.64, Y.68, L.86 Ligand excluded by PLIP FMT.16: 3 residues within 4Å: Chain A: K.5, E.285, F.286 Ligand excluded by PLIP FMT.17: 1 residues within 4Å: Chain A: L.305 Ligand excluded by PLIP FMT.18: 2 residues within 4Å: Chain A: Q.400 Ligands: FMT.19 Ligand excluded by PLIP FMT.19: 4 residues within 4Å: Chain A: T.356, L.367, W.405 Ligands: FMT.18 Ligand excluded by PLIP FMT.20: 3 residues within 4Å: Chain A: P.127, R.130, K.343 Ligand excluded by PLIP FMT.21: 3 residues within 4Å: Chain A: Y.163, P.179, I.180 Ligand excluded by PLIP FMT.22: 4 residues within 4Å: Chain A: W.3, N.55, E.71, P.72 Ligand excluded by PLIP FMT.23: 5 residues within 4Å: Chain A: K.48, S.220, A.221, V.223, N.224 Ligand excluded by PLIP FMT.24: 4 residues within 4Å: Chain A: A.2, W.3, E.82, P.83 Ligand excluded by PLIP FMT.25: 6 residues within 4Å: Chain A: T.24, Q.27, A.28, A.185, L.186, K.188 Ligand excluded by PLIP FMT.26: 5 residues within 4Å: Chain A: V.217, G.313, S.314, S.363, S.364 Ligand excluded by PLIP FMT.27: 3 residues within 4Å: Chain A: F.286, K.287, E.288 Ligand excluded by PLIP FMT.28: 6 residues within 4Å: Chain A: L.105, A.109, I.139, S.360, V.361, G.362 Ligand excluded by PLIP FMT.29: 4 residues within 4Å: Chain A: V.325, L.326, W.327, N.328 Ligand excluded by PLIP

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.30: 17 residues within 4Å: Chain A: H.17, D.19, H.20, G.21, K.22, T.23, T.24, W.33, N.149, K.150, D.152, V.153, S.184, A.185, L.186 Ligands: FMT.7, MG.31 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:D.19, A:H.20, A:G.21, A:K.22, A:T.23, A:T.24, A:T.24, A:N.149, A:K.150, A:K.150, A:S.184, A:A.185, A:L.186 Water bridges: A:K.22, A:K.22, A:E.40 Salt bridges: A:K.22, A:D.152

2 x MG: MAGNESIUM ION(Non-covalent)

MG.31: 2 residues within 4Å: Chain A: T.23 Ligands: GDP.30 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.23, H2O.12, H2O.12, H2O.12, H2O.12 MG.32: 1 residues within 4Å: Chain A: H.187 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.187, H2O.17

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

NA.33: 4 residues within 4Å: Chain A: E.66, Y.68, V.69, S.76 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.66, A:S.76 NA.34: 2 residues within 4Å: Chain A: V.151, V.154 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.154 NA.35: 1 residues within 4Å: Chain A: M.111 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.111 NA.36: 2 residues within 4Å: Chain A: T.54, T.70 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.54, A:T.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nikonov, O. et al., Conformational transitions in the gamma subunit of the archaeal translation initiation factor 2. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-03-12

Peptides

Translation initiation factor 2 subunit gamma: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Translation initiation factor 2 subunit gamma

Related Entries With Identical Sequence