SMTL ID : 5obw.1

Mycoplasma genitalium DnaK-NBD in complex with ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.1: 2 residues within 4Å: Ligands: ADP.2, PO4.3 No protein-ligand interaction detected (PLIP)

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 20 residues within 4Å: Chain A: G.14, T.15, T.16, N.17, G.179, G.180, 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, PO4.3 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:T.16, A:T.16, A:N.17, A:N.17, A:G.180, A:E.247, A:K.250, A:S.254, A:S.254, A:G.322 Water bridges: A:T.16, A:G.181, A:G.321, A:D.349, A:D.349

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 8 residues within 4Å: Chain A: G.14, T.15, K.72, P.126, E.154, T.182 Ligands: MG.1, ADP.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:T.15, A:E.154, A:T.182, A:T.182, A:T.182 Water bridges: A:E.154, A:E.154, A:E.154, A:G.179, A:G.180, A:D.184 Salt bridges: A:K.72

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

SO4.4: 1 residues within 4Å: Chain A: R.295 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.295 SO4.5: 4 residues within 4Å: Chain A: K.138, E.149, R.150, I.151 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.151, A:I.151 Salt bridges: A:K.138 SO4.6: 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 SO4.7: 3 residues within 4Å: Chain A: V.29, V.30, R.38 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.30 Water bridges: A:R.38, A:R.38, A:R.38 Salt bridges: A:R.38 SO4.8: 2 residues within 4Å: Chain A: R.169, N.315 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.315 Salt bridges: A:R.169

1 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.9: 4 residues within 4Å: Chain A: S.45, I.52, Q.60, N.64 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.60

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 7 residues within 4Å: Chain A: T.15, K.72, R.73, Y.128, F.129, T.182, N.204 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.15, A:Y.128, A:N.204 Water bridges: A:K.72, A:R.73 GOL.11: 8 residues within 4Å: Chain A: L.7, M.23, G.361, R.364, G.365, D.366, H.369, H.370 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.364, A:G.365 Water bridges: A:M.23, A:M.23, A:G.25 GOL.12: 5 residues within 4Å: Chain A: Y.128, T.200, A.201, G.202, N.204 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.200, A:T.200, A:N.204 Water bridges: A:D.203, A:D.203 GOL.13: 3 residues within 4Å: Chain A: S.254, A.255, R.282 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.254, A:R.282, A:R.282

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

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