SMTL ID : 4tmt.2 (2 other biounits)

Translation initiation factor eIF5B (517-858) mutant D533A from C. thermophilum, bound to GTPgammaS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

monomer

Ligands

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

GSP.1: 22 residues within 4Å: Chain A: H.18, V.19, A.20, T.21, G.22, K.23, T.24, K.25, Q.36, G.42, I.43, T.44, P.83, G.84, N.135, K.136, D.138, R.139, S.203, A.204, H.205 Ligands: MG.2 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:H.18, A:A.20, A:T.21, A:G.22, A:K.23, A:K.23, A:T.24, A:K.25, A:Q.36, A:T.44, A:T.44, A:G.84, A:H.85, A:N.135, A:K.136, A:K.136, A:A.204, A:H.205 Water bridges: A:T.24, A:E.39 Salt bridges: A:K.23, A:D.138 pi-Stacking: A:H.205 pi-Cation interactions: A:K.136, A:H.205

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.24, T.44 Ligands: GSP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.24, A:T.44, H2O.3, H2O.3

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: L.8, P.75, K.305 Ligands: EDO.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.8 Water bridges: A:D.6, A:K.305 EDO.4: 3 residues within 4Å: Chain A: D.6, K.305 Ligands: EDO.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.305 Water bridges: A:K.5, A:D.6 EDO.5: 7 residues within 4Å: Chain A: Q.46, I.47, L.240, E.241, K.243, D.253, R.293 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.47, A:E.241, A:K.243, A:D.253 Water bridges: A:L.240 EDO.6: 8 residues within 4Å: Chain A: P.286, R.290, E.291, L.292, I.294, G.296, Q.297, Y.298 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.292, A:Q.297, A:Q.297, A:Y.298 EDO.7: 4 residues within 4Å: Chain A: K.174, N.183, S.184, E.185 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.183, A:S.184 EDO.8: 4 residues within 4Å: Chain A: V.64, N.65, K.66, D.67 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.63, A:K.66, A:D.67, A:D.67 EDO.9: 5 residues within 4Å: Chain A: S.233, L.235, G.259, I.260, R.262 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.235, A:I.260, A:R.262, A:R.262

1 x ACY: ACETIC ACID(Non-functional Binders)

ACY.10: 5 residues within 4Å: Chain A: Y.51, T.285, P.288, H.301, Q.308 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.308 Salt bridges: A:H.301

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 5 residues within 4Å: Chain A: I.30, R.31, Q.32, K.60, M.289 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kuhle, B. et al., A monovalent cation acts as structural and catalytic cofactor in translational GTPases. Embo J. (2014)

Release Date

2014-09-24

Peptides

eIF5B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

eIF5B

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