SMTL ID : 7mzg.1

SARS-CoV-2 receptor binding domain bound to Fab PDI 42

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG-NAG-FUC.1: 5 residues within 4Å: Chain C: F.8, G.9, F.12, N.13, L.38 No protein-ligand interaction detected (PLIP)

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: G.55, S.56, T.57 Chain C: T.85 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.85, A:T.57 GOL.3: 6 residues within 4Å: Chain B: Q.37, P.59, R.61, F.62, E.81, D.82 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.37, B:Q.37, B:E.81, B:D.82 GOL.4: 6 residues within 4Å: Chain A: V.167, H.168 Chain B: T.166, E.167, Q.168, D.169 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:V.167, A:H.168, B:D.169 Water bridges: A:T.169, B:E.167, B:E.167, B:Q.168, B:S.170, B:T.174 GOL.5: 11 residues within 4Å: Chain A: F.170, P.171, V.173, S.181, L.182, S.183 Chain B: Q.162, S.164, S.178, S.179, T.180 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:P.171, A:S.181, A:S.183, B:Q.162, B:S.164, B:T.180 GOL.6: 4 residues within 4Å: Chain A: Y.102 Chain B: Y.49 Chain C: G.155, F.156 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Y.49 Water bridges: B:Q.55, B:Q.55, B:Q.55, C:N.157 GOL.7: 5 residues within 4Å: Chain C: F.12, N.13, S.43, F.44, W.106 No protein-ligand interaction detected (PLIP)

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

PDI 42 heavy chain: A
PDI 42 light chain: B
Spike protein S1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
A

PDI 42 heavy chain

PDI 42 light chain

Spike protein S1

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