SMTL ID : 7q0g.1

Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-49 and FI-3A Fabs

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

hetero-1-1-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-FUC.1: 12 residues within 4Å: Chain A: N.25, A.26, S.53, A.54, L.123 Chain D: Y.50, T.57 Chain E: S.100, A.103, I.105, F.107 Ligands: GOL.3 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:A.103, E:I.105, E:F.107

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: S.57, T.58, G.86, Y.190 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.58 GOL.3: 5 residues within 4Å: Chain A: F.24, N.25, S.55 Chain E: W.102 Ligands: NAG-NAG-BMA-MAN-FUC.1 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:N.25, A:S.55, A:S.55, E:W.102 GOL.4: 6 residues within 4Å: Chain A: R.139, S.141, N.142, L.143, K.144, E.147 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.139, A:R.139, A:S.141, A:N.142, A:K.144 GOL.5: 4 residues within 4Å: Chain A: L.174, Q.175, S.176 Chain B: R.101 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.101, A:Q.175, A:S.176 GOL.11: 9 residues within 4Å: Chain B: S.35, V.37, W.47, A.96, D.98, N.105, W.107 Chain C: Y.36, Q.89 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:S.35, B:W.47, C:Y.36, C:Q.89, C:Q.89 Water bridges: B:H.99 GOL.12: 6 residues within 4Å: Chain B: D.61, S.62, V.63, K.64, R.66, R.86 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.63, B:R.86, B:R.86 GOL.13: 4 residues within 4Å: Chain B: G.137, G.138, T.139, P.189 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.138, B:S.190 GOL.15: 5 residues within 4Å: Chain B: W.47, Y.59, D.61 Chain C: L.94, P.95 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.61 Water bridges: B:D.61 GOL.22: 7 residues within 4Å: Chain B: V.167, H.168 Chain C: T.164, E.165, D.167, T.172 Ligands: K.27 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:T.164, C:D.167, B:H.168 GOL.30: 4 residues within 4Å: Chain D: R.110, N.140, D.172, T.174 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.140 GOL.31: 7 residues within 4Å: Chain D: Q.39, K.40, P.41, G.42, Q.43 Chain E: Q.39 Ligands: TAR.39 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:K.40, D:G.42 Water bridges: D:Q.39, D:Q.39, E:A.40 GOL.32: 7 residues within 4Å: Chain D: Q.38, R.46, P.60, R.62, F.63, E.82, D.83 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.38, D:R.46, D:R.46, D:D.83, D:D.83 GOL.40: 4 residues within 4Å: Chain E: N.160, A.163, L.164, Q.197 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.160, E:A.163, E:Q.197

14 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 4 residues within 4Å: Chain A: K.166, Y.171, F.172 Chain B: R.101 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain A: N.36 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: S.151, T.152 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: F.111, T.112 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain B: S.25, G.26 Ligand excluded by PLIP CL.23: 1 residues within 4Å: Chain C: T.20 Ligand excluded by PLIP CL.24: 1 residues within 4Å: Chain C: A.1 Ligand excluded by PLIP CL.33: 3 residues within 4Å: Chain D: Y.33, G.93, T.94 Ligand excluded by PLIP CL.34: 2 residues within 4Å: Chain D: R.46, L.47 Ligand excluded by PLIP CL.35: 1 residues within 4Å: Chain D: R.55 Ligand excluded by PLIP CL.41: 4 residues within 4Å: Chain D: T.99, F.100 Chain E: E.46, W.47 Ligand excluded by PLIP CL.42: 1 residues within 4Å: Chain E: G.44 Ligand excluded by PLIP CL.43: 2 residues within 4Å: Chain E: V.126, K.214 Ligand excluded by PLIP CL.44: 4 residues within 4Å: Chain E: E.10, K.12, V.18, K.19 Ligand excluded by PLIP

14 x K: POTASSIUM ION(Non-covalent)

K.10: 1 residues within 4Å: Chain A: F.29 No protein-ligand interaction detected (PLIP) K.17: 2 residues within 4Å: Chain B: A.40, G.44 No protein-ligand interaction detected (PLIP) K.18: 4 residues within 4Å: Chain A: K.140 Chain B: S.30, S.53, R.71 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Metal complexes: B:S.30, A:K.140 K.19: 2 residues within 4Å: Chain B: Q.3, L.4 No protein-ligand interaction detected (PLIP) K.20: 1 residues within 4Å: Chain B: M.112 No protein-ligand interaction detected (PLIP) K.21: 5 residues within 4Å: Chain B: F.170, L.182, S.183 Chain C: S.162, S.176 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.176, H2O.4, H2O.6 K.25: 2 residues within 4Å: Chain C: Q.37, K.45 No protein-ligand interaction detected (PLIP) K.26: 2 residues within 4Å: Chain C: V.146, E.161 No protein-ligand interaction detected (PLIP) K.27: 7 residues within 4Å: Chain B: H.168 Chain C: N.138, T.164, T.172, Y.173, S.174 Ligands: GOL.22 No protein-ligand interaction detected (PLIP) K.28: 1 residues within 4Å: Chain C: S.67 No protein-ligand interaction detected (PLIP) K.29: 1 residues within 4Å: Chain C: G.212 No protein-ligand interaction detected (PLIP) K.36: 8 residues within 4Å: Chain D: T.166, E.167, D.169, T.174, Y.175, S.176 Chain E: H.169 Ligands: K.37 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:T.166, D:E.167, H2O.9 K.37: 3 residues within 4Å: Chain D: D.169 Chain E: H.169 Ligands: K.36 No protein-ligand interaction detected (PLIP) K.45: 1 residues within 4Å: Chain D: Y.88 No protein-ligand interaction detected (PLIP)

3 x TAR: D(-)-TARTARIC ACID(Non-covalent)

TAR.14: 9 residues within 4Å: Chain B: Y.149, E.152, P.153, V.154, T.169, F.170, P.171, A.172, L.182 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.154, B:A.172 TAR.38: 8 residues within 4Å: Chain E: E.153, P.154, V.155, T.170, F.171, P.172, A.173, L.183 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:Y.150, E:E.153, E:V.155, E:A.173 Water bridges: E:V.155, E:V.157 TAR.39: 6 residues within 4Å: Chain D: G.42 Chain E: V.93, Y.95, Q.110, G.111 Ligands: GOL.31 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Y.95, E:G.111 Water bridges: E:Q.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, C. et al., The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. Cell Host Microbe (2022)

Release Date

2021-12-22

Peptides

Spike protein S1: A
FI-3A Fab heavy chain: B
FI-3A Fab light chain: C
Beta-49 Fab light chain: D
Beta-49 Fab heavy chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
H

C
L

D
B

E
A

Spike protein S1

FI-3A Fab heavy chain

FI-3A Fab light chain

Beta-49 Fab light chain

Beta-49 Fab heavy chain

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