SMTL ID : 7n1r.1 (1 other biounit)

A novel and unique ATP hydrolysis to AMP by a human Hsp70 BiP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

monomer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 2 residues within 4Å: Chain A: K.330, N.357 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.357, A:N.357 Water bridges: A:K.330 GOL.2: 2 residues within 4Å: Chain A: R.363, G.364 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.363, A:G.364 Water bridges: A:I.365, A:I.365, A:I.365 GOL.3: 4 residues within 4Å: Chain A: L.528, R.531, I.532, R.535 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.535, A:R.535 Water bridges: A:E.50 GOL.4: 3 residues within 4Å: Chain A: M.316, K.317, Q.320 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.317, A:Q.320

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

SO4.5: 3 residues within 4Å: Chain A: H.242, K.303, L.307 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.245, A:K.303, A:K.303 Salt bridges: A:H.242, A:K.303 SO4.6: 5 residues within 4Å: Chain A: K.253, D.254, K.257, Y.290, E.291 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.290, A:Y.290 Water bridges: A:K.253, A:D.254, A:K.257, A:E.291 Salt bridges: A:K.253, A:K.257

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

PO4.7: 6 residues within 4Å: Chain A: D.71, D.88, F.91, E.233, D.234, Q.237 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.71, A:E.233 Water bridges: A:R.74 Salt bridges: A:R.74 PO4.8: 1 residues within 4Å: Chain A: K.321 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.321, A:K.321, A:K.321, A:K.321 Salt bridges: A:K.321 PO4.9: 3 residues within 4Å: Chain A: R.443, P.444, D.448 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.448 Water bridges: A:D.448, A:D.448 Salt bridges: A:R.443 PO4.10: 2 residues within 4Å: Chain A: Q.159, K.162 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.159 Water bridges: A:D.163 Salt bridges: A:K.162 PO4.11: 5 residues within 4Å: Chain A: E.2, V.4, H.144, N.171, M.173 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.171 Water bridges: A:E.2, A:E.2, A:E.2 Salt bridges: A:H.144 PO4.12: 5 residues within 4Å: Chain A: A.185, G.364, I.365, N.366, Y.373 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.366 PO4.13: 3 residues within 4Å: Chain A: Q.279, A.282, R.283 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.279, A:R.283, A:R.283 PO4.16: 9 residues within 4Å: Chain A: G.13, T.14, K.73, E.178, G.203, G.204, G.205, T.206 Ligands: MG.14 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:T.14, A:E.178, A:G.203, A:G.204, A:G.205, A:T.206, A:T.206 Water bridges: A:E.178, A:E.178, A:E.178 Salt bridges: A:K.73

1 x MG: MAGNESIUM ION(Non-covalent)

MG.14: 7 residues within 4Å: Chain A: G.13, T.14, T.15, Y.16, G.204 Ligands: AMP.15, PO4.16 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: AMP.15

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.15: 17 residues within 4Å: Chain A: T.15, Y.16, G.203, G.204, G.232, E.270, K.273, R.274, S.277, G.340, G.341, S.342, R.344, I.345, P.367, D.368 Ligands: MG.14 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Y.16, A:G.203, A:E.270, A:K.273, A:R.274, A:S.277, A:G.341, A:R.344, A:P.367 Water bridges: A:R.274, A:R.274, A:D.368

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.17: 1 residues within 4Å: Chain A: R.26 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, H. et al., A novel and unique ATP hydrolysis to AMP by a human Hsp70 Binding immunoglobin protein (BiP). Protein Sci. (2022)

Release Date

2022-01-12

Peptides

Endoplasmic reticulum chaperone BiP: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Endoplasmic reticulum chaperone BiP

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