SMTL ID : 6yla.2 (1 other biounit)

Crystal structure of the SARS-CoV-2 receptor binding domain in complex with CR3022 Fab

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

hetero-1-1-1-mer

Ligands

6 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 4 residues within 4Å: Chain A: N.17, S.47, F.48, W.110 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:W.110 DMS.3: 3 residues within 4Å: Chain A: G.78, D.79, Y.182 No protein-ligand interaction detected (PLIP) DMS.5: 7 residues within 4Å: Chain A: V.56, S.57, K.60, L.61, L.64 Chain C: Y.55, W.56 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.57 DMS.10: 4 residues within 4Å: Chain B: L.46, W.48 Chain C: T.103, F.104 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:F.104, B:W.48 DMS.12: 2 residues within 4Å: Chain C: L.15, S.174 No protein-ligand interaction detected (PLIP) DMS.13: 4 residues within 4Å: Chain A: D.101 Chain C: Y.31, Y.98, S.99 No protein-ligand interaction detected (PLIP)

1 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.2: 5 residues within 4Å: Chain A: W.27, N.28, R.29, F.138, R.140 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.29, A:F.138, A:R.140, A:R.140

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

NAG.4: 4 residues within 4Å: Chain A: F.12, G.13, N.17, V.41 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.12

7 x MLI: MALONATE ION(Non-functional Binders)

MLI.6: 3 residues within 4Å: Chain B: S.120, F.151, L.180 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.151, B:L.180 MLI.7: 2 residues within 4Å: Chain A: R.82 Chain B: E.58 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:E.58 Salt bridges: A:K.52 MLI.8: 2 residues within 4Å: Chain B: T.1 Chain C: S.62 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:T.1, B:T.1, C:S.62 MLI.9: 4 residues within 4Å: Chain B: T.10, Q.112, G.113, T.115 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.10, B:T.115, B:T.115, B:T.115 MLI.14: 3 residues within 4Å: Chain C: V.197, A.199, S.214 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.214 MLI.15: 4 residues within 4Å: Chain C: V.156, Q.161, D.191, H.195 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.156 Hydrogen bonds: C:Q.161, C:D.191 Salt bridges: C:H.195 MLI.16: 2 residues within 4Å: Chain C: V.197, N.216 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.197 Hydrogen bonds: C:N.216

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.11: 13 residues within 4Å: Chain B: Q.40, G.43, K.44, I.94 Chain C: D.9, Q.44, K.45, P.46, G.47, V.91, Y.93, Q.106, G.107 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huo, J. et al., Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike. Cell Host Microbe (2020)

Release Date

2020-04-15

Peptides

Spike glycoprotein: A
Heavy Chain: B
Light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

Heavy Chain

Light chain

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