SMTL ID : 4m53.1

Gamma subunit of the translation initiation factor 2 from Sulfolobus solfataricus in complex with GDPCP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.1: 6 residues within 4Å: Chain A: T.34, S.35, K.36, G.39, Y.40, R.208 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.35, A:K.36 Water bridges: A:W.33

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

FMT.2: 3 residues within 4Å: Chain A: A.331, K.332, R.393 Ligand excluded by PLIP FMT.3: 5 residues within 4Å: Chain A: Y.195, R.196, D.197, Q.200, I.232 Ligand excluded by PLIP FMT.4: 4 residues within 4Å: Chain A: T.193, P.194, Y.195, R.196 Ligand excluded by PLIP FMT.5: 6 residues within 4Å: Chain A: L.94, A.98, I.128, S.349, V.350, G.351 Ligand excluded by PLIP FMT.6: 4 residues within 4Å: Chain A: V.47, K.53, Y.57, L.75 Ligand excluded by PLIP FMT.7: 5 residues within 4Å: Chain A: K.336, V.337, D.338, R.388, I.390 Ligand excluded by PLIP FMT.8: 3 residues within 4Å: Chain A: M.347, T.354 Ligands: FMT.13 Ligand excluded by PLIP FMT.9: 2 residues within 4Å: Chain A: E.333, M.334 Ligand excluded by PLIP FMT.10: 5 residues within 4Å: Chain A: L.301, G.302, S.353, T.354, R.373 Ligand excluded by PLIP FMT.11: 4 residues within 4Å: Chain A: R.119, V.123, F.158, V.329 Ligand excluded by PLIP FMT.12: 3 residues within 4Å: Chain A: P.313, L.315 Ligands: NA.29 Ligand excluded by PLIP FMT.13: 5 residues within 4Å: Chain A: T.355, L.356, R.372, R.373 Ligands: FMT.8 Ligand excluded by PLIP FMT.14: 6 residues within 4Å: Chain A: W.3, N.44, T.59, E.60, P.61 Ligands: FMT.17 Ligand excluded by PLIP FMT.15: 2 residues within 4Å: Chain A: E.241, K.264 Ligand excluded by PLIP FMT.16: 4 residues within 4Å: Chain A: R.269, G.271, D.272 Ligands: GCP.26 Ligand excluded by PLIP FMT.17: 3 residues within 4Å: Chain A: N.44, R.77 Ligands: FMT.14 Ligand excluded by PLIP FMT.18: 3 residues within 4Å: Chain A: W.316, E.370, L.371 Ligand excluded by PLIP FMT.19: 5 residues within 4Å: Chain A: I.32, Y.40, A.41, E.42, G.271 Ligand excluded by PLIP FMT.20: 4 residues within 4Å: Chain A: K.201, Q.233, W.378, S.379 Ligand excluded by PLIP FMT.21: 3 residues within 4Å: Chain A: T.30, G.31 Ligands: NA.28 Ligand excluded by PLIP FMT.22: 2 residues within 4Å: Chain A: P.116, K.332 Ligand excluded by PLIP FMT.23: 3 residues within 4Å: Chain A: N.110, E.111, K.139 Ligand excluded by PLIP FMT.24: 8 residues within 4Å: Chain A: M.90, A.91, L.94, M.347, S.387, W.394, R.395, M.396 Ligand excluded by PLIP

2 x GCP: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER(Non-covalent)

GCP.25: 18 residues within 4Å: Chain A: V.18, D.19, H.20, G.21, K.22, T.23, T.24, W.33, P.84, G.85, N.138, K.139, D.141, V.142, S.173, A.174, L.175 Ligands: MG.27 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:D.19, A:H.20, A:G.21, A:K.22, A:K.22, A:T.23, A:T.24, A:T.24, A:G.85, A:N.138, A:K.139, A:K.139, A:S.173, A:A.174, A:L.175 Water bridges: A:T.23, A:T.23, A:T.23, A:H.86 Salt bridges: A:D.141 GCP.26: 12 residues within 4Å: Chain A: K.36, F.210, V.212, K.223, V.226, S.267, I.268, R.269, G.271, A.285, G.287 Ligands: FMT.16 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:K.36, A:K.223, A:S.267, A:S.267, A:G.271, A:A.285, A:G.287 Water bridges: A:K.214, A:K.214, A:K.214, A:R.269, A:R.269, A:R.269, A:R.269, A:D.298 Salt bridges: A:K.214 pi-Cation interactions: A:R.269, A:R.269

1 x MG: MAGNESIUM ION(Non-covalent)

MG.27: 2 residues within 4Å: Chain A: T.23 Ligands: GCP.25 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.23, H2O.1, H2O.3, H2O.24

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

NA.28: 4 residues within 4Å: Chain A: T.30, T.43, T.59 Ligands: FMT.21 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.43, A:T.59, A:T.59 Water bridges: A:N.44 NA.29: 3 residues within 4Å: Chain A: V.312, P.313 Ligands: FMT.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.312 Water bridges: A:V.312 NA.30: 2 residues within 4Å: Chain A: M.100 Ligands: NA.36 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.100 Water bridges: A:D.101 NA.31: 2 residues within 4Å: Ligands: NA.34, NA.35 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.157 NA.32: 4 residues within 4Å: Chain A: E.55, Y.57, V.58, D.181 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.57 NA.33: 2 residues within 4Å: Chain A: W.316, N.317 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.317, A:N.317 NA.34: 1 residues within 4Å: Ligands: NA.31 No protein-ligand interaction detected (PLIP) NA.35: 4 residues within 4Å: Chain A: Q.157, F.158, K.160 Ligands: NA.31 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.160 NA.36: 1 residues within 4Å: Ligands: NA.30 No protein-ligand interaction detected (PLIP)

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

2013-08-28

Peptides

Translation initiation factor 2 subunit gamma: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Translation initiation factor 2 subunit gamma