SMTL ID : 4tmv.2 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

monomer

Ligands

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

GSP.1: 23 residues within 4Å: Chain A: H.18, V.19, D.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, NA.3 33 PLIP interactions: 33 interactions with chain A Hydrogen bonds: A:H.18, A:D.20, A:T.21, A:G.22, A:K.23, A:K.23, A:T.24, A:T.24, A:K.25, A:K.25, A:K.25, A:Q.36, A:T.44, A:G.84, A:N.135, A:K.136, A:K.136, A:S.203, A:A.204, A:H.205 Water bridges: A:Q.36, A:G.42, A:T.44, A:T.44, A:H.85, A:D.138, A:D.138, A:H.205 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

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

NA.3: 3 residues within 4Å: Chain A: D.20, G.42 Ligands: GSP.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.20 Water bridges: A:T.44

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: K.29, I.30, Q.32, K.60, N.148, I.210, P.211 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.29, A:Q.32, A:K.60 Water bridges: A:Q.59, A:K.60, A:K.60, A:N.148, A:N.148 GOL.5: 5 residues within 4Å: Chain A: R.266, V.329, G.330, P.331, E.335 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.266, A:R.266 Water bridges: A:V.329 GOL.6: 4 residues within 4Å: Chain A: K.277, T.278, P.315, G.316 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.278 Water bridges: A:K.277, A:R.281

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
A

eIF5B

Related Entries With Identical Sequence