SMTL ID : 4zu9.1

Crystal structure of bacterial selenocysteine-specific elongation factor EF-Sec

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.19 Å

Oligo State

monomer

Ligands

1 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.1: 20 residues within 4Å: Chain A: V.12, D.13, H.14, G.15, K.16, T.17, T.18, G.38, L.39, S.40, V.62, P.63, G.64, K.117, D.119, K.120, S.150, A.151, V.152 Ligands: MG.2 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:D.13, A:D.13, A:D.13, A:H.14, A:G.15, A:K.16, A:K.16, A:T.17, A:T.18, A:T.18, A:S.40, A:S.40, A:G.64, A:K.117, A:K.117, A:A.151, A:V.152 Salt bridges: A:D.119

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.17, S.40, D.61 Ligands: GNP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.17, A:S.40

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: V.233, K.234, K.235 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.234, A:K.235, A:K.235 SO4.4: 3 residues within 4Å: Chain A: K.548, T.554, R.555 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.554, A:R.555 Salt bridges: A:K.548, A:R.555 SO4.5: 3 residues within 4Å: Chain A: R.579, K.581, R.582 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.582, A:R.582 Salt bridges: A:R.579

1 x CYS: CYSTEINE(Non-covalent)

CYS.6: 5 residues within 4Å: Chain A: R.30, R.198, H.229, G.230, R.241 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.229, A:G.230, A:R.241 Salt bridges: A:H.229

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Itoh, Y. et al., Crystal structure of the full-length bacterial selenocysteine-specific elongation factor SelB. Nucleic Acids Res. (2015)

Release Date

2015-09-23

Peptides

Elongation factor SelB: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Elongation factor SelB