SMTL ID : 7a4u.1

Crystal structure of lid-truncated apo BiP in an oligomeric state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-dimer

Ligands

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 11 residues within 4Å: Chain A: G.10, T.11, K.70, P.147, E.175, G.200, G.201, G.202, A.203, D.205 Ligands: GOL.6 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.11, A:T.11, A:K.70, A:G.201, A:G.202, A:A.203, A:D.205 Water bridges: A:Y.149, A:E.175 GOL.2: 5 residues within 4Å: Chain A: D.152, R.155, Q.156, K.159, I.172 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.156, A:K.159 Water bridges: A:K.159, A:I.172 GOL.3: 5 residues within 4Å: Chain A: E.472, T.474, E.476, T.486, E.488 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.474, A:E.476, A:E.488 Water bridges: A:K.420, A:E.488 GOL.4: 3 residues within 4Å: Chain A: V.393, R.413, N.414 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.413, A:N.414, A:N.414 GOL.5: 2 residues within 4Å: Chain A: R.413, N.414 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.413 Water bridges: A:N.414, A:N.414 GOL.6: 9 residues within 4Å: Chain A: G.10, T.11, T.12, Y.13, G.200, G.201, G.338, D.365 Ligands: GOL.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.12, A:Y.13, A:Y.13, A:G.201, A:G.338, A:D.365 GOL.7: 11 residues within 4Å: Chain B: G.10, T.11, K.70, P.147, E.175, G.200, G.201, G.202, A.203, D.205 Ligands: GOL.12 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:T.11, B:K.70, B:G.201, B:G.202, B:A.203, B:D.205, B:D.205 Water bridges: B:T.11, B:D.198 GOL.8: 5 residues within 4Å: Chain B: D.152, R.155, Q.156, K.159, I.172 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.156, B:K.159 Water bridges: B:K.159, B:I.172 GOL.9: 5 residues within 4Å: Chain B: E.472, T.474, E.476, T.486, E.488 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.472, B:E.476 Water bridges: B:K.420, B:T.474 GOL.10: 7 residues within 4Å: Chain A: S.422, Q.423, I.424, E.472 Chain B: V.393, R.413, N.414 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.423, A:E.472, A:E.472, B:R.413, B:N.414, B:N.414 GOL.11: 3 residues within 4Å: Chain A: Q.470 Chain B: R.413, N.414 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.413 Water bridges: B:N.414, B:N.414 GOL.12: 9 residues within 4Å: Chain B: G.10, T.11, T.12, Y.13, G.200, G.201, G.338, D.365 Ligands: GOL.7 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.12, B:Y.13, B:Y.13, B:G.201, B:G.338, B:D.365, B:D.365

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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