SMTL ID : 8qrg.1

SARS-CoV-2 delta RBD complexed with XBB-2 Fab and NbC1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 3 residues within 4Å: Chain A: G.13, F.16, N.17 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.16

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: F.21, A.22, S.23, N.124, Y.125 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.124 Water bridges: A:S.23, A:S.23, A:S.23 GOL.3: 8 residues within 4Å: Chain A: K.91 Chain C: L.50, E.98, P.100, R.101 Chain D: S.91, D.92, L.94 6 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: C:E.98, C:R.101, D:D.92, D:D.92, A:K.91 Water bridges: C:Y.52 GOL.4: 5 residues within 4Å: Chain A: V.177, Y.182 Chain B: T.106, W.107, P.108 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.106, B:T.106, A:Y.182 GOL.5: 3 residues within 4Å: Chain D: Q.37, P.59, F.62 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.37 GOL.6: 4 residues within 4Å: Chain C: Y.107, W.108 Chain D: P.44, N.45 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:W.108, D:P.44, D:N.45 Water bridges: C:V.2, D:L.46 GOL.7: 8 residues within 4Å: Chain D: I.83, K.103, V.104, E.105, R.142, E.165, Q.166, Y.173 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:E.105, D:R.142, D:E.165, D:Q.166, D:Q.166, D:Y.173

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, C. et al., A structure-function analysis shows SARS-CoV-2 BA.2.86 balances antibody escape and ACE2 affinity. Cell Rep Med (2024)

Release Date

2024-05-08

Peptides

Spike protein S1: A
NbC1: B
XBB-2 heavy chain: C
XBB-2 light chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
A

C
H

D
L

Spike protein S1

NbC1

XBB-2 heavy chain

XBB-2 light chain

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