SMTL ID : 6cbv.1

Crystal structure of BRIL bound to an affinity matured synthetic antibody.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: S.55, S.58, S.60, Y.104, W.105 Chain C: K.77 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:S.55, A:S.55, A:S.58, A:S.60, A:W.105, C:K.77, C:K.77 Water bridges: C:D.74 GOL.4: 6 residues within 4Å: Chain B: Q.38, K.46, G.58, V.59, P.60, F.63 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.58 Water bridges: B:Q.38, B:Q.38

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 6 residues within 4Å: Chain A: Y.53, T.61, S.62 Chain B: Y.94 Chain C: K.77, N.80 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Y.53, A:T.61, A:S.62, C:N.80 FMT.5: 6 residues within 4Å: Chain A: F.136, K.157, D.158 Chain B: Q.126, S.129, T.131 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.126, B:S.129, B:T.131, A:D.158 Water bridges: A:K.157

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 3 residues within 4Å: Chain B: L.183, S.184, D.187 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.184, B:S.184

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mukherjee, S. et al., Synthetic antibodies against BRIL as universal fiducial marks for single-particle cryoEM structure determination of membrane proteins. Nat Commun (2020)

Release Date

2019-02-06

Peptides

Heavy chain, Fab fragment: A
Light Chain, Fab fragment: B
BRIL: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
B

Heavy chain, Fab fragment

Light Chain, Fab fragment

BRIL

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