SMTL ID : 7mzk.2 (1 other biounit)

SARS-CoV-2 receptor binding domain bound to Fab WCSL 129 and Fab PDI 96

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-1-1-1-1-1-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: 4 residues within 4Å: Chain C: G.9, N.13, L.38 Chain E: N.35 No protein-ligand interaction detected (PLIP)

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 7 residues within 4Å: Chain A: P.41, K.106, K.167, P.168, S.169, K.170, Y.176 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.176 Hydrogen bonds: A:P.168, A:P.168, A:K.170, A:Y.176 Water bridges: A:T.108 Salt bridges: A:K.106, A:K.106, A:K.167, A:K.167, A:K.170, A:K.170

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain D: K.12, A.16, S.17 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.17, D:S.17

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

WCSL 129 light chain: A
WCSL 129 heavy chain: B
Spike protein S1: C
PDI 96 heavy chain: D
PDI 96 light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
A

D
H

E
L

WCSL 129 light chain

WCSL 129 heavy chain

Spike protein S1

PDI 96 heavy chain

PDI 96 light chain

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