SMTL ID : 5obx.1

Mycoplasma genitalium DnaK-NBD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

monomer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: K.138, R.150, I.151 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.151, A:I.151 Water bridges: A:K.138, A:K.138 Salt bridges: A:K.138 SO4.2: 3 residues within 4Å: Chain A: N.204, R.205 Ligands: PGE.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.204 Salt bridges: A:R.205 SO4.3: 2 residues within 4Å: Chain A: N.130, D.131 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.131, A:D.131 Water bridges: A:D.131, A:A.132 SO4.4: 5 residues within 4Å: Chain A: Y.128, D.184, G.202, D.203, N.204 5 PLIP interactions: 5 interactions with chain A Water bridges: A:G.202, A:D.203, A:D.203, A:N.204, A:N.204 SO4.5: 6 residues within 4Å: Chain A: G.14, T.15, T.16, N.17, G.179, G.180 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.15, A:T.16, A:T.16, A:N.17, A:N.17, A:G.180 Water bridges: A:T.15, A:K.72, A:T.182 SO4.6: 3 residues within 4Å: Chain A: V.29, V.30, R.38 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.30 Water bridges: A:R.38, A:R.38 Salt bridges: A:R.38 SO4.7: 3 residues within 4Å: Chain A: K.116, R.364, D.366 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.364 Salt bridges: A:K.116, A:R.364

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.8: 5 residues within 4Å: Chain A: S.70, R.73, L.74, R.205 Ligands: SO4.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.70, A:R.205 Water bridges: A:S.70, A:R.73

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 6 residues within 4Å: Chain A: T.15, K.72, R.73, Y.128, F.129, N.204 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.15, A:Y.128 GOL.10: 5 residues within 4Å: Chain A: Y.162, G.163, I.164, A.167, E.316 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.316 GOL.11: 1 residues within 4Å: Chain A: M.237 2 PLIP interactions: 2 interactions with chain A Water bridges: A:M.237, A:M.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Adell, M. et al., The nucleotide-bound/substrate-bound conformation of the Mycoplasma genitalium DnaK chaperone. Protein Sci. (2018)

Release Date

2018-05-09

Peptides

Chaperone protein DnaK: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Chaperone protein DnaK