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

Crystal structure of eukaryotic translation initiation factor eIF5B (517-858) from Chaetomium thermophilum in complex with GTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

monomer

Ligands

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

GTP.1: 23 residues within 4Å: Chain A: V.19, D.20, T.21, G.22, K.23, T.24, K.25, Q.36, G.42, I.43, T.44, T.82, G.84, H.85, N.135, K.136, D.138, R.139, S.203, A.204, H.205 Ligands: MG.2, NA.3 29 PLIP interactions: 29 interactions with chain A Hydrogen bonds: A:H.18, A:D.20, A:T.21, A:T.21, A:G.22, A:K.23, A:T.24, A:K.25, A:Q.36, 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:Q.36, A:T.44, A:T.44, A:T.44, A:H.205 Salt bridges: A:K.23, 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: GTP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.24, A:T.44, H2O.1, H2O.1

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

NA.3: 4 residues within 4Å: Chain A: D.20, G.42, I.43 Ligands: GTP.1 4 PLIP interactions: 4 interactions with chain A Water bridges: A:D.20, A:E.39, A:G.41, A:T.44

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

ACY.4: 3 residues within 4Å: Chain A: G.259, I.260, R.262 4 PLIP interactions: 4 interactions with chain A Water bridges: A:I.260, A:R.262, A:R.262 Salt bridges: A:R.262

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: L.8, V.54, K.58, F.72, K.73, V.74, P.75 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.58, A:K.58 GOL.6: 6 residues within 4Å: Chain A: K.25, D.28, K.29, T.33, N.34, A.204 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.25, A:D.28, A:E.37 GOL.7: 6 residues within 4Å: Chain A: K.29, I.30, Q.32, K.60, I.210, P.211 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.32 Water bridges: A:Q.59, A:K.60, A:K.60, A:N.148 GOL.8: 6 residues within 4Å: Chain A: T.33, N.34, V.35, R.290, E.291, I.294 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.34, A:E.291

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kuhle, B. et al., eIF5B employs a novel domain release mechanism to catalyze ribosomal subunit joining. Embo J. (2014)

Release Date

2014-07-09

Peptides

Eukaryotic translation initiation factor 5B-like protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Eukaryotic translation initiation factor 5B-like protein

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