SMTL ID : 4rd1.1

Structure of aIF2-gamma H97A variant from Sulfolobus solfataricus bound to GTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.1: 22 residues within 4Å: Chain A: H.17, V.18, D.19, H.20, G.21, K.22, T.23, T.24, M.45, T.46, G.96, N.149, K.150, D.152, V.153, S.184, A.185, L.186 Ligands: GDP.2, MG.3, MG.4, PO4.5 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:D.19, A:D.19, A:H.20, A:G.21, A:K.22, A:T.23, A:T.23, A:T.24, A:T.24, A:T.46, A:G.96, A:N.149, A:K.150, A:K.150, A:S.184, A:A.185, A:L.186 Water bridges: A:T.23, A:T.46, A:A.97, A:D.152, A:H.187 Salt bridges: A:K.22, A:K.22, A:D.152

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

GDP.2: 19 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: GTP.1, MG.3, MG.4, PO4.5 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:D.19, A:D.19, A:H.20, A:G.21, A:K.22, A:T.23, 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:T.23, A:T.46, A:T.46, A:T.46, A:D.152, A:H.187 Salt bridges: A:K.22, A:D.152 GDP.6: 11 residues within 4Å: Chain A: F.221, V.223, K.225, K.234, V.237, S.278, I.279, R.280, G.282, A.296, G.298 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.278, A:S.278, A:G.282, A:A.296, A:G.298 Water bridges: A:R.280, A:R.280, A:R.280 Salt bridges: A:K.225, A:K.225 pi-Cation interactions: A:R.280

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: T.23, T.46 Ligands: GTP.1, GDP.2, PO4.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.23, A:T.46, H2O.1, H2O.1 MG.4: 6 residues within 4Å: Chain A: D.19, G.44, M.45 Ligands: GTP.1, GDP.2, PO4.5 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.19, A:G.44, H2O.2, H2O.4, H2O.12, H2O.12

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 12 residues within 4Å: Chain A: V.18, D.19, K.22, M.45, T.46, P.95, G.96, A.97 Ligands: GTP.1, GDP.2, MG.3, MG.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.19, A:T.46, A:G.96, A:A.97 Water bridges: A:D.19, A:D.19, A:T.23 Salt bridges: A:K.22

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.7: 1 residues within 4Å: Chain A: K.287 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.287 MPD.8: 1 residues within 4Å: Chain A: Y.300 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.300, A:Y.300

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dubiez, E. et al., Identification of a second GTP-bound magnesium ion in archaeal initiation factor 2. Nucleic Acids Res. (2015)

Release Date

2015-05-27

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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