SMTL ID : 4tmt.3 (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

homo-dimer

Ligands

2 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 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:A.20, A:T.21, A:T.21, A:G.22, A:K.23, A:K.23, A:T.24, A:K.25, A:K.25, A:K.25, A:Q.36, A:T.44, A:T.44, A:G.84, A:N.135, A:K.136, A:K.136, A:A.204, A:H.205 Water bridges: A:T.24, A:H.85, A:D.138 Salt bridges: A:K.23, A:D.138 pi-Stacking: A:H.205 pi-Cation interactions: A:K.136, A:H.205 GSP.10: 22 residues within 4Å: Chain B: 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.11 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:H.18, B:A.20, B:T.21, B:G.22, B:K.23, B:K.23, B:T.24, B:K.25, B:Q.36, B:T.44, B:T.44, B:G.84, B:H.85, B:N.135, B:K.136, B:K.136, B:A.204, B:H.205 Water bridges: B:T.24, B:E.39 Salt bridges: B:K.23, B:D.138 pi-Stacking: B:H.205 pi-Cation interactions: B:K.136, B:H.205

2 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 MG.11: 3 residues within 4Å: Chain B: T.24, T.44 Ligands: GSP.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.24, B:T.44, H2O.17, H2O.17

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

EDO.3: 5 residues within 4Å: Chain A: G.181, F.182, N.183, R.195, Y.196 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.183 EDO.4: 6 residues within 4Å: Chain A: K.29, I.30, Q.32, K.60, N.148, I.210 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.32, A:G.207 Water bridges: A:K.60 EDO.5: 4 residues within 4Å: Chain A: K.191, N.192, F.193, A.194 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.192, A:F.193, A:A.194 EDO.6: 8 residues within 4Å: Chain A: I.108, M.109, H.110, G.111, R.169, Q.172, V.173, Q.176 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.110, A:R.169, A:Q.176 EDO.7: 5 residues within 4Å: Chain A: E.86, S.87, F.88, S.89 Chain B: K.58 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.86, A:S.89 Water bridges: B:Q.59 EDO.12: 4 residues within 4Å: Chain B: L.8, P.75, K.305 Ligands: EDO.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.8 Water bridges: B:D.6, B:K.305 EDO.13: 3 residues within 4Å: Chain B: D.6, K.305 Ligands: EDO.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.305 Water bridges: B:K.5, B:D.6 EDO.14: 7 residues within 4Å: Chain B: Q.46, I.47, L.240, E.241, K.243, D.253, R.293 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.47, B:E.241, B:K.243, B:D.253 Water bridges: B:L.240 EDO.15: 8 residues within 4Å: Chain B: P.286, R.290, E.291, L.292, I.294, G.296, Q.297, Y.298 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.292, B:Q.297, B:Q.297, B:Y.298 EDO.16: 4 residues within 4Å: Chain B: K.174, N.183, S.184, E.185 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.183, B:S.184 EDO.17: 4 residues within 4Å: Chain B: V.64, N.65, K.66, D.67 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.63, B:K.66, B:D.67, B:D.67 EDO.18: 5 residues within 4Å: Chain B: S.233, L.235, G.259, I.260, R.262 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.235, B:I.260, B:R.262, B:R.262

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

CL.8: 3 residues within 4Å: Chain A: P.129, F.130, R.224 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain B: I.30, R.31, Q.32, K.60, M.289 Ligand excluded by PLIP

1 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.9: 8 residues within 4Å: Chain A: C.221, Q.222, E.223, R.224, M.225, A.226, S.227, M.230 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.73, A:Q.222

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

ACY.19: 5 residues within 4Å: Chain B: Y.51, T.285, P.288, H.301, Q.308 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.308 Salt bridges: B:H.301

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

eIF5B

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