SMTL ID : 5oby.1

Mycoplasma genitalium DnaK-NBD in complex with AMP-PNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: D.177 Ligands: ANP.2 No protein-ligand interaction detected (PLIP)

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.2: 22 residues within 4Å: Chain A: G.14, T.15, T.16, N.17, G.179, G.180, G.181, T.182, G.208, D.209, E.247, K.250, I.251, S.254, G.321, G.322, S.323, R.325, M.326, D.349 Ligands: MG.1, GOL.3 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:T.15, A:T.16, A:T.16, A:N.17, A:G.179, A:G.180, A:G.181, A:T.182, A:T.182, A:E.247, A:K.250, A:S.254, A:S.254, A:G.322 Water bridges: A:D.12, A:T.15, A:E.154, A:E.154, A:T.182, A:T.182, A:G.321

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: N.17, T.39, K.58, E.247, D.349 Ligands: ANP.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.58, A:E.247, A:D.349, A:D.349 Water bridges: A:N.17, A:N.17, A:K.58, A:K.58 GOL.4: 7 residues within 4Å: Chain A: T.15, K.72, R.73, Y.128, F.129, T.182, N.204 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.15, A:Y.128, A:N.204 GOL.5: 1 residues within 4Å: Chain A: R.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.150, A:R.150 Water bridges: A:Q.359

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

SO4.6: 3 residues within 4Å: Chain A: V.29, V.30, R.38 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.30 Salt bridges: A:R.38 SO4.7: 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 SO4.8: 1 residues within 4Å: Chain A: P.65 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.63

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

Related Entries With Identical Sequence