SMTL ID : 7raq.1

Crystal structure of CV3-25 Fab bound to SARS-CoV-2 spike stem helix peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

hetero-1-1-1-mer

Ligands

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 2 residues within 4Å: Chain A: K.87, S.89 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.89 GOL.3: 4 residues within 4Å: Chain A: K.155, Q.183, S.184, S.185 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.155, A:K.155, A:S.184, A:S.185, A:S.185 Water bridges: A:S.185 GOL.4: 6 residues within 4Å: Chain A: V.175, H.176 Chain B: T.164, E.165, D.167, S.168 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:H.176, B:D.167, B:S.168, B:S.168 Water bridges: A:T.177, A:T.177, A:T.177, B:E.165, B:E.165 GOL.5: 9 residues within 4Å: Chain A: P.100, W.111, D.113 Chain B: L.46, Y.49, Q.55 Chain C: D.15, V.16, D.17 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: A:W.111, A:D.113, C:D.17, B:Y.49 GOL.7: 10 residues within 4Å: Chain A: F.178, P.179, S.189, L.190, S.191 Chain B: Q.160, S.162, S.176, S.177, T.178 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:F.178, A:S.191, B:Q.160, B:S.162, B:T.178, B:T.178 GOL.8: 4 residues within 4Å: Chain A: P.135 Chain B: S.121, D.122, E.123 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.122, B:E.123, B:E.123, B:E.123 GOL.9: 3 residues within 4Å: Chain A: Y.102, C.103 Chain C: T.12 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.12, A:C.103 Water bridges: C:T.12

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

SO4.2: 5 residues within 4Å: Chain A: Y.27, T.28, R.31, Y.32 Chain C: P.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.28, A:R.31, A:Y.32, A:Y.32 SO4.6: 2 residues within 4Å: Chain A: R.31 Chain C: L.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hurlburt, N.K. et al., Structural definition of a pan-sarbecovirus neutralizing epitope on the spike S2 subunit. Commun Biol (2022)

Release Date

2022-04-13

Peptides

CV3-25 Fab Heavy Chain: A
CV3-25 Fab Light Chain: B
spike stem helix peptide: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
P

CV3-25 Fab Heavy Chain

CV3-25 Fab Light Chain

spike stem helix peptide