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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

DMS.1: 6 residues within 4Å: Chain A: F.16, N.17, S.47, F.48, W.110 Ligands: NAG.7 2 PLIP interactions: 2 interactions with chain A pi-Cation interactions: A:W.110, A:W.110 DMS.2: 3 residues within 4Å: Chain A: G.78, V.177, Y.182 No protein-ligand interaction detected (PLIP) DMS.4: 3 residues within 4Å: Chain A: W.27, R.29, R.140 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:W.27 DMS.5: 3 residues within 4Å: Chain A: R.20, F.21, N.28 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.28 DMS.10: 3 residues within 4Å: Chain B: N.209, T.210, K.211 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.211 DMS.11: 2 residues within 4Å: Chain B: K.206, P.207 No protein-ligand interaction detected (PLIP) DMS.14: 6 residues within 4Å: Chain A: V.56, S.57, K.60 Chain B: T.105 Chain C: Y.55, W.56 No protein-ligand interaction detected (PLIP) DMS.15: 5 residues within 4Å: Chain B: L.46, E.47, W.48 Chain C: T.103, F.104 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:F.104

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

MLI.3: 3 residues within 4Å: Chain A: Y.123, Q.167, S.168 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.168 MLI.8: 3 residues within 4Å: Chain A: R.82 Chain B: D.56, E.58 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.52, A:R.82, A:R.82 Hydrophobic interactions: B:E.58 MLI.9: 3 residues within 4Å: Chain B: S.120, G.179, L.180 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.180 Hydrogen bonds: B:S.120 MLI.12: 3 residues within 4Å: Chain B: L.175, Q.176, S.177 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.175 MLI.13: 3 residues within 4Å: Chain B: P.154, T.156, K.206 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.206 Salt bridges: B:K.206, B:K.206

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

NAG.6: 2 residues within 4Å: Chain A: T.2, N.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.2 NAG.7: 3 residues within 4Å: Chain A: N.17, V.41 Ligands: DMS.1 No protein-ligand interaction detected (PLIP)

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

1PE.16: 12 residues within 4Å: Chain B: Q.40, G.43, K.44, Y.96 Chain C: D.9, Q.44, P.46, G.47, V.91, Y.93, Q.106, G.107 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.9, C:G.47, C:Y.93

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
E

B
H

C
L

Spike glycoprotein

Heavy Chain

Light chain

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