SMTL ID : 6i5m.1

Gamma subunit of the translation initiation factor 2 from Sulfolobus solfataricus in complex with GDP and formate ion

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

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

GDP.1: 17 residues within 4Å: Chain A: H.17, D.19, H.20, G.21, K.22, T.23, T.24, E.40, N.149, K.150, D.152, V.153, S.184, A.185, L.186 Ligands: FMT.7, MG.19 17 PLIP interactions: 17 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:E.40, A:N.149, A:K.150, A:K.150, A:A.185, A:L.186 Water bridges: A:K.22, A:K.22 Salt bridges: A:K.22, A:D.152

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

FMT.2: 6 residues within 4Å: Chain A: V.18, M.45, T.46, P.95, G.96, H.97 Ligand excluded by PLIP FMT.3: 5 residues within 4Å: Chain A: S.314, V.361, S.364, V.386, A.387 Ligand excluded by PLIP FMT.4: 6 residues within 4Å: Chain A: V.217, D.222, G.313, S.314, S.363, S.364 Ligand excluded by PLIP FMT.5: 3 residues within 4Å: Chain A: L.336, E.337, R.338 Ligand excluded by PLIP FMT.6: 5 residues within 4Å: Chain A: R.219, S.220, V.237, T.306, K.307 Ligand excluded by PLIP FMT.7: 3 residues within 4Å: Chain A: N.121, K.150 Ligands: GDP.1 Ligand excluded by PLIP FMT.8: 3 residues within 4Å: Chain A: L.186, H.187, K.188 Ligand excluded by PLIP FMT.9: 4 residues within 4Å: Chain A: Y.333, L.335, P.350, I.351 Ligand excluded by PLIP FMT.10: 5 residues within 4Å: Chain A: T.365, T.366, L.367, R.383, R.384 Ligand excluded by PLIP FMT.11: 4 residues within 4Å: Chain A: E.344, L.346, I.401, A.402 Ligand excluded by PLIP FMT.12: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP FMT.13: 1 residues within 4Å: Chain A: E.158 Ligand excluded by PLIP FMT.14: 3 residues within 4Å: Chain A: A.342, K.343, E.344 Ligand excluded by PLIP FMT.15: 3 residues within 4Å: Chain A: Y.163, P.179, I.180 Ligand excluded by PLIP FMT.16: 6 residues within 4Å: Chain A: V.339, K.347, V.348, D.349, R.399, I.401 Ligand excluded by PLIP FMT.17: 3 residues within 4Å: Chain A: K.36, H.37, S.38 Ligand excluded by PLIP FMT.18: 2 residues within 4Å: Chain A: K.234, Y.300 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.19: 2 residues within 4Å: Chain A: T.23 Ligands: GDP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.23, H2O.1, H2O.1, H2O.9 MG.20: 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.12

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

NA.21: 2 residues within 4Å: Chain A: V.151, V.154 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.151, A:V.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nikonov, O. et al., The third structural switch in the archaeal translation initiation factor 2 (aIF2) molecule and its possible role in the initiation of GTP hydrolysis and the removal of aIF2 from the ribosome. Acta Crystallogr D Struct Biol (2019)

Release Date

2019-01-02

Peptides

Translation initiation factor 2 subunit gamma: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Translation initiation factor 2 subunit gamma

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