SMTL ID : 7mzi.1

SARS-CoV-2 receptor binding domain bound to Fab WCSL 129

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 2 residues within 4Å: Chain C: G.9, N.13 No protein-ligand interaction detected (PLIP)

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: T.118, V.119, T.120, L.139, I.140, S.141 Chain B: F.170, T.187 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.118, A:T.120 GOL.3: 5 residues within 4Å: Chain A: P.14, S.81, V.109, L.110, G.111 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.81 Water bridges: A:S.81 GOL.4: 3 residues within 4Å: Chain A: P.60, R.62 Ligands: GOL.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.62 Water bridges: A:Q.80 GOL.5: 8 residues within 4Å: Chain A: Q.38, K.46, P.60, R.62, F.63, E.82, D.83 Ligands: GOL.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.38, A:K.46, A:K.46, A:R.62, A:D.83, A:D.83 GOL.6: 4 residues within 4Å: Chain B: F.27, T.28, R.31, F.32 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.28 GOL.7: 7 residues within 4Å: Chain B: V.2, Q.3, L.4, I.106, W.107, G.108, Q.109 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.4, B:L.4, B:Q.109 Water bridges: B:W.107, B:Q.109 GOL.8: 3 residues within 4Å: Chain B: P.41, V.173, L.174 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.172, B:L.174, B:L.174 GOL.9: 6 residues within 4Å: Chain B: Y.60, K.65, G.66, R.67, F.68, T.69 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.66, B:F.68, B:F.68, B:F.68, B:T.69 GOL.10: 3 residues within 4Å: Chain B: K.210, V.211, D.212 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.212, B:D.212 GOL.11: 4 residues within 4Å: Chain B: K.121, G.122, P.123, S.124 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.121, B:S.124 Water bridges: B:G.122 GOL.12: 7 residues within 4Å: Chain A: L.47, Y.50, P.56 Chain B: G.100, W.101, D.105 Chain C: Q.163 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:D.105, C:Q.163, C:Q.163 GOL.14: 7 residues within 4Å: Chain A: D.53, Q.54, R.55 Chain C: R.73, D.75, E.76, K.87 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:R.73, C:R.73, C:E.76, C:K.87, A:Q.54 Water bridges: C:Q.79, C:Y.175, A:D.53, A:D.53, A:R.55 GOL.15: 5 residues within 4Å: Chain C: R.73, Y.165, F.167, N.171, Y.175 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.73, C:N.171, C:Y.175 Water bridges: C:R.73 GOL.16: 5 residues within 4Å: Chain C: F.12, N.13, S.43, F.44, W.106 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.43

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.13: 9 residues within 4Å: Chain C: R.25, Y.66, P.96, D.98, F.99, T.100, F.134, F.185, E.186 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.25, C:D.98, C:T.100, C:E.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wheatley, A.K. et al., Landscape of human antibody recognition of the SARS-CoV-2 receptor binding domain. Cell Rep (2021)

Release Date

2021-10-06

Peptides

WCSL 129 light chain: A
WCSL 129 heavy chain: B
Spike protein S1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
A

WCSL 129 light chain

WCSL 129 heavy chain

Spike protein S1

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