SMTL ID : 7mzm.1

SARS-CoV-2 receptor binding domain bound to Fab PDI 215

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 5 residues within 4Å: Chain C: F.8, G.9, F.12, N.13, S.41 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.8, C:F.12

2 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.2: 5 residues within 4Å: Chain C: G.86, K.87, D.90, Y.91 Ligands: IPA.3 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:K.87, C:Y.91 Hydrogen bonds: C:K.87 IPA.3: 4 residues within 4Å: Chain C: K.87, L.125, F.126 Ligands: IPA.2 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.125, C:F.126 Hydrogen bonds: C:K.87, C:L.125

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 215 heavy chain: A
PDI 215 light chain: B
Spike protein S1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
A

PDI 215 heavy chain

PDI 215 light chain

Spike protein S1

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