SMTL ID : 6zyh.1

Crystal structure of GRP78 (70kDa heat shock protein 5 / BiP) ATPase domain in complex with ADP and calcium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 17 residues within 4Å: Chain A: G.9, T.10, T.11, Y.12, G.199, G.200, G.228, E.266, K.269, R.270, S.273, G.336, G.337, S.338, R.340, I.341 Ligands: CA.3 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:T.10, A:T.11, A:Y.12, A:G.200, A:G.201, A:E.266, A:K.269, A:R.270, A:R.270, A:S.273, A:G.337 Water bridges: A:T.10, A:T.10, A:T.10, A:R.270, A:R.340 ADP.4: 18 residues within 4Å: Chain B: G.9, T.10, T.11, Y.12, G.199, G.200, G.228, E.266, K.269, R.270, S.273, G.336, G.337, S.338, R.340, I.341, D.364 Ligands: CA.5 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:T.11, B:Y.12, B:G.200, B:G.201, B:G.228, B:E.266, B:K.269, B:R.270, B:S.273, B:G.337 Water bridges: B:T.10, B:T.10, B:T.10

4 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.2: 3 residues within 4Å: Chain A: H.225, D.230 Chain B: G.288 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.225, A:D.230, H2O.2, H2O.5, H2O.8 CA.3: 1 residues within 4Å: Ligands: ADP.1 No protein-ligand interaction detected (PLIP) CA.5: 1 residues within 4Å: Ligands: ADP.4 No protein-ligand interaction detected (PLIP) CA.6: 2 residues within 4Å: Chain B: H.225, D.230 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.225, B:D.230, B:D.230, H2O.7, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Preissler, S. et al., Calcium depletion challenges endoplasmic reticulum proteostasis by destabilising BiP-substrate complexes. Elife (2020)

Release Date

2020-12-16

Peptides

Endoplasmic reticulum chaperone BiP: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Endoplasmic reticulum chaperone BiP