SMTL ID : 4jn4.1

Allosteric opening of the polypeptide-binding site when an Hsp70 binds ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: E.171 Ligands: ATP.2 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain B: E.171 Ligands: ATP.11 No protein-ligand interaction detected (PLIP)

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 20 residues within 4Å: Chain A: G.10, T.11, T.12, N.13, K.70, E.171, G.196, G.197, G.198, A.199, G.229, E.267, K.270, I.271, S.274, G.341, G.342, Q.343, R.345 Ligands: MG.1 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:T.11, A:T.11, A:T.12, A:T.12, A:N.13, A:N.13, A:N.13, A:E.171, A:G.196, A:G.197, A:G.198, A:A.199, A:A.199, A:E.267, A:E.267, A:K.270, A:S.274, A:S.274, A:G.342 Water bridges: A:K.70, A:K.70, A:E.171 Salt bridges: A:K.70 ATP.11: 20 residues within 4Å: Chain B: G.10, T.11, T.12, N.13, K.70, E.171, G.196, G.197, G.198, A.199, G.229, E.267, K.270, I.271, S.274, G.341, G.342, Q.343, R.345 Ligands: MG.10 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:T.11, B:T.11, B:T.12, B:N.13, B:N.13, B:N.13, B:G.196, B:G.197, B:G.198, B:A.199, B:A.199, B:E.267, B:K.270, B:S.274, B:S.274, B:G.342 Water bridges: B:E.230, B:D.368, B:D.368 Salt bridges: B:K.70

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

SO4.3: 4 residues within 4Å: Chain A: R.25, R.34 Chain B: N.366 Ligands: GOL.8 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Water bridges: A:V.26, A:R.34, B:N.366 Salt bridges: A:R.25, A:R.34 Hydrogen bonds: B:N.366 SO4.4: 2 residues within 4Å: Chain A: R.441, K.442 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.442 Water bridges: A:R.441, A:R.443 Salt bridges: A:R.441 SO4.5: 3 residues within 4Å: Chain A: G.184, R.188, R.362 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.184 Salt bridges: A:R.188, A:R.362 SO4.6: 4 residues within 4Å: Chain A: S.427, M.428, G.429, G.430 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.427, A:M.428, A:G.430 SO4.7: 1 residues within 4Å: Chain A: R.463 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.463 SO4.12: 4 residues within 4Å: Chain A: N.366 Chain B: R.25, R.34 Ligands: GOL.18 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:N.366 Water bridges: A:N.366, A:N.366, A:N.366, A:E.369, B:R.25, B:R.34, B:R.34 Salt bridges: B:R.25, B:R.34 SO4.13: 2 residues within 4Å: Chain A: K.268 Chain B: R.56 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.56, A:K.268 SO4.14: 3 residues within 4Å: Chain B: G.184, R.188, R.362 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.184 Salt bridges: B:R.188, B:R.362 SO4.15: 4 residues within 4Å: Chain B: S.427, M.428, G.429, G.430 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.427, B:M.428, B:G.430 SO4.16: 1 residues within 4Å: Chain B: R.463 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.463 SO4.17: 3 residues within 4Å: Chain B: E.440, R.441, K.442 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.440, B:K.442 Water bridges: B:R.441, B:R.443 Salt bridges: B:R.441

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 12 residues within 4Å: Chain A: R.25, V.26, L.27, E.28, R.34, Y.130 Chain B: K.363, D.364, V.365, N.366, P.367 Ligands: SO4.3 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:V.365, A:R.25, A:E.28, A:R.34 GOL.9: 6 residues within 4Å: Chain A: R.84, D.231, R.235, D.311, L.312, R.315 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.231, A:R.235, A:R.315, A:R.315 Water bridges: A:R.84 GOL.18: 12 residues within 4Å: Chain A: K.363, D.364, V.365, N.366, P.367 Chain B: R.25, V.26, L.27, E.28, R.34, Y.130 Ligands: SO4.12 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.25, B:V.26, B:E.28, B:R.34, A:V.365 Water bridges: A:K.363 GOL.19: 5 residues within 4Å: Chain B: R.84, D.231, R.235, L.312, R.315 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.231, B:D.231, B:R.235, B:R.235, B:R.315 Water bridges: B:R.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qi, R. et al., Allosteric opening of the polypeptide-binding site when an Hsp70 binds ATP. Nat.Struct.Mol.Biol. (2013)

Release Date

2013-05-29

Peptides

Chaperone protein DnaK: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Chaperone protein DnaK

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