SMTL ID : 7yzn.1

Structure of C-terminally truncated aIF5B from Pyrococcus abyssi complexed with GTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: K.39, T.40, T.60 Ligands: GTP.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.40, A:T.60, H2O.1, H2O.3

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

GTP.2: 24 residues within 4Å: Chain A: H.34, V.35, D.36, H.37, G.38, K.39, T.40, T.41, A.52, I.59, T.60, P.99, G.100, H.101, N.151, K.152, D.154, R.155, S.219, A.220, K.221, Y.222 Ligands: MG.1, NA.3 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:D.36, A:G.38, A:K.39, A:T.40, A:T.41, A:T.41, A:T.60, A:G.100, A:H.101, A:N.151, A:K.152, A:K.152, A:S.219, A:A.220, A:K.221 Water bridges: A:T.40, A:E.55, A:T.60, A:K.221 Salt bridges: A:K.39, A:K.39, A:D.154

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

NA.3: 4 residues within 4Å: Chain A: D.36, G.58, I.59 Ligands: GTP.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.36 Water bridges: A:T.60

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