SMTL ID : 7a4v.1

Crystal structure of lid-truncated ADP-bound BiP in an oligomeric state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 19 residues within 4Å: Chain A: G.10, T.11, T.12, Y.13, G.200, G.201, G.229, E.230, E.267, K.270, R.271, S.274, G.337, G.338, S.339, R.341, I.342, D.365 Ligands: K.4 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:T.12, A:Y.13, A:G.201, A:G.202, A:E.267, A:K.270, A:R.271, A:S.274, A:G.338, A:R.341 Water bridges: A:D.8, A:T.11, A:T.11, A:T.12, A:K.55, A:A.203, A:D.365 ADP.5: 19 residues within 4Å: Chain B: G.10, T.11, T.12, Y.13, G.200, G.201, G.229, E.230, E.267, K.270, R.271, S.274, G.337, G.338, S.339, R.341, I.342, D.365 Ligands: K.8 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:T.12, B:Y.13, B:G.201, B:G.202, B:E.267, B:E.267, B:K.270, B:R.271, B:S.274, B:G.338, B:R.341 Water bridges: B:D.8, B:T.11, B:T.11, B:T.12, B:Y.13, B:K.55, B:A.203, B:D.365

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: K.420, E.472, T.474, E.476, T.486, E.488 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.420, A:E.472, A:T.474, A:T.486, A:E.488 Water bridges: A:T.474, A:T.486 GOL.3: 2 residues within 4Å: Chain A: D.518, K.521 No protein-ligand interaction detected (PLIP) GOL.6: 6 residues within 4Å: Chain B: K.420, E.472, T.474, E.476, T.486, E.488 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.420, B:E.472, B:E.472 Water bridges: B:T.474, B:T.486 GOL.7: 2 residues within 4Å: Chain B: D.518, K.521 No protein-ligand interaction detected (PLIP)

2 x K: POTASSIUM ION(Non-covalent)

K.4: 4 residues within 4Å: Chain A: D.8, G.10, Y.13 Ligands: ADP.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.8, A:Y.13, H2O.4, H2O.6, H2O.9 K.8: 4 residues within 4Å: Chain B: D.8, G.10, Y.13 Ligands: ADP.5 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.8, B:Y.13, H2O.16, H2O.18, H2O.21

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
A

Endoplasmic reticulum chaperone BiP

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