SMTL ID : 7yyp.1

Structure of aIF5B from Pyrococcus abyssi complexed with GDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

monomer

Ligands

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

GDP.1: 14 residues within 4Å: Chain A: H.34, D.36, H.37, G.38, K.39, T.40, T.41, N.151, K.152, D.154, R.155, S.219, A.220, K.221 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:D.36, A:H.37, A:G.38, A:K.39, A:T.40, A:T.40, A:T.40, A:T.41, A:T.41, A:N.151, A:K.152, A:R.155, A:R.155, A:A.220, A:K.221 Salt bridges: A:K.39, A:D.154 pi-Cation interactions: A:K.152

5 x NO3: NITRATE ION(Non-functional Binders)

NO3.2: 3 residues within 4Å: Chain A: E.163, K.221, Y.222 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.163, A:E.163 NO3.3: 3 residues within 4Å: Chain A: P.264, G.265, G.267 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.265, A:G.267 NO3.4: 1 residues within 4Å: Chain A: E.352 No protein-ligand interaction detected (PLIP) NO3.5: 4 residues within 4Å: Chain A: P.145, F.146, E.212, Y.240 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.146, A:E.212 NO3.6: 3 residues within 4Å: Chain A: F.486, R.516, T.591 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kazan, R. et al., Role of aIF5B in archaeal translation initiation. Nucleic Acids Res. (2022)

Release Date

2022-06-29

Peptides

Probable translation initiation factor IF-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Probable translation initiation factor IF-2