SMTL ID : 7r6w.1

SARS-CoV-2 spike receptor-binding domain (RBD) in complex with S2X35 Fab and S309 Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

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

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 7 residues within 4Å: Chain A: Y.50, R.55, T.57 Chain E: G.16, N.20, V.44, L.45 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.57

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

SO4.2: 3 residues within 4Å: Chain A: P.8, G.9, T.10 Ligand excluded by PLIP SO4.3: 4 residues within 4Å: Chain A: P.60, D.61, R.62, R.78 Ligand excluded by PLIP SO4.4: 1 residues within 4Å: Chain A: R.108 Ligand excluded by PLIP SO4.5: 5 residues within 4Å: Chain A: S.121, D.122, E.123 Chain B: P.137, K.228 Ligand excluded by PLIP SO4.6: 2 residues within 4Å: Chain A: T.57, G.58 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain A: G.42, Q.43, A.44 Chain B: Q.119 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain B: I.51, G.56, T.71, T.72 Ligand excluded by PLIP SO4.13: 2 residues within 4Å: Chain B: R.85, R.87 Ligand excluded by PLIP SO4.14: 2 residues within 4Å: Chain B: T.207, K.224 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain A: T.164, E.165, D.167 Chain B: H.178 Ligand excluded by PLIP SO4.16: 1 residues within 4Å: Chain B: S.109 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain C: R.17, T.19 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain C: K.68, S.69, G.70 Ligand excluded by PLIP SO4.19: 2 residues within 4Å: Chain C: R.56, S.65 Ligand excluded by PLIP SO4.20: 1 residues within 4Å: Chain C: R.56 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain C: Y.51, P.57, S.58 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain C: V.162, K.163, A.164 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain C: Q.174, S.175 Chain D: H.179 Ligand excluded by PLIP SO4.25: 5 residues within 4Å: Chain D: Y.27, T.28, N.31, Y.32, Q.102 Ligand excluded by PLIP SO4.26: 7 residues within 4Å: Chain D: N.31, Y.32, G.33, Y.101, Y.106, D.107, I.110 Ligand excluded by PLIP SO4.27: 5 residues within 4Å: Chain E: G.153, S.154, T.155, F.163, N.164 Ligand excluded by PLIP SO4.28: 2 residues within 4Å: Chain E: R.32, R.143 Ligand excluded by PLIP SO4.32: 4 residues within 4Å: Chain E: P.103, D.104, D.105, P.140 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 3 residues within 4Å: Chain A: S.53, S.54, R.55 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.53, A:R.55, A:R.55 GOL.8: 11 residues within 4Å: Chain A: Q.160, S.162, S.176, S.177, T.178 Chain B: F.180, P.181, V.183, S.191, L.192, S.193 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.162, A:S.177, A:T.178, B:F.180, B:S.191, B:S.193 GOL.11: 7 residues within 4Å: Chain A: S.95, L.96 Chain B: W.47, W.50, N.59, T.101, R.102 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.101, B:T.101, B:R.102, A:S.95 Water bridges: B:N.59

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

CL.10: 2 residues within 4Å: Chain A: S.95 Chain B: Q.62 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain D: G.149, T.150 Ligand excluded by PLIP CL.31: 4 residues within 4Å: Chain C: Y.33, D.34 Chain D: Y.112 Chain E: R.85 Ligand excluded by PLIP

2 x POL: N-PROPANOL(Non-covalent)

POL.29: 4 residues within 4Å: Chain D: F.108 Chain E: S.52, Y.185 Ligands: POL.30 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.52, E:S.52, E:Y.185 POL.30: 5 residues within 4Å: Chain E: S.50, S.52, W.113, N.114 Ligands: POL.29 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.52, E:N.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Starr, T.N. et al., SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape. Nature (2021)

Release Date

2021-07-21

Peptides

Light Chain of Fab domain of monoclonal antibody S309: A
Heavy Chain of Fab domain of monoclonal antibody S309: B
Light Chain of Fab domain of monoclonal antibody S2X35: C
Heavy Chain of Fab domain of monoclonal antibody S2X35: D
Spike protein S1: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
L

D
H

E
R

Light Chain of Fab domain of monoclonal antibody S309

Heavy Chain of Fab domain of monoclonal antibody S309

Light Chain of Fab domain of monoclonal antibody S2X35

Heavy Chain of Fab domain of monoclonal antibody S2X35

Spike protein S1

Related Entries With Identical Sequence