SMTL ID : 8be1.2 (1 other biounit)

SARS-CoV-2 RBD in complex with a Fab fragment of a neutralising antibody mRBD2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: G.67, K.68, R.85, S.86 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.67 Water bridges: A:K.68 Salt bridges: A:K.68 SO4.2: 3 residues within 4Å: Chain A: Y.60 Chain C: G.156, F.157 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:F.157 SO4.3: 3 residues within 4Å: Chain A: Y.101, Y.102, Y.103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.101 SO4.4: 7 residues within 4Å: Chain A: V.158, T.159, W.160, G.163, L.165, S.166, V.169 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.158, A:W.160, A:G.163, A:L.165 SO4.5: 6 residues within 4Å: Chain A: A.204, H.205, P.206, S.209, T.210, K.211 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.205, A:T.210, A:T.210 Salt bridges: A:K.211 SO4.6: 7 residues within 4Å: Chain A: L.46, E.47, W.48, N.62 Chain B: W.97, T.98, F.99 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:W.48, A:W.48, A:N.62, B:F.99 SO4.7: 4 residues within 4Å: Chain B: E.155, R.156, Q.157, N.158 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.155, B:Q.157, B:N.158, B:N.158 Salt bridges: B:R.156 SO4.8: 5 residues within 4Å: Chain A: P.132 Chain B: V.116, S.117, I.118, K.208 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.118 Salt bridges: B:K.208 SO4.9: 4 residues within 4Å: Chain C: G.173, V.174, G.175, Y.176 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.175, C:Y.176 SO4.10: 5 residues within 4Å: Chain C: R.74, Y.166, G.167, F.168, Y.176 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.167 Salt bridges: C:R.74 SO4.11: 5 residues within 4Å: Chain C: P.97, D.99, F.100, T.101, F.135 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fischer, K. et al., Microfluidics-enabled fluorescence-activated cell sorting of single pathogen-specific antibody secreting cells for the rapid discovery of monoclonal antibodies. Biorxiv (2023)

Release Date

2023-01-25

Peptides

Antibody heavy chain: A
Antibody light chain: B
Spike protein S1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

Antibody heavy chain

Antibody light chain

Spike protein S1

Related Entries With Identical Sequence