SMTL ID : 8d47.2 (1 other biounit)

fp.006 Fab in complex with SARS-CoV-2 Fusion Peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 10 residues within 4Å: Chain A: A.9, V.85, Y.87, G.101, G.102, K.104 Chain B: Q.39, G.42, K.43, G.44 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.39, A:G.102 Water bridges: B:G.44 PEG.2: 7 residues within 4Å: Chain B: Q.39, A.40, P.41, G.42, G.92, V.93, L.125 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.42

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 4 residues within 4Å: Chain A: E.166, D.168 Chain B: V.180, H.181 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.166, A:D.168, B:V.180 Water bridges: A:T.165, A:T.165, A:S.169, A:S.169, A:K.170, A:K.170, B:T.182 Salt bridges: B:H.181 PO4.4: 2 residues within 4Å: Chain B: R.87, E.89 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.89, B:E.89 Salt bridges: B:R.87 PO4.5: 4 residues within 4Å: Chain A: T.56 Chain B: R.98, D.118, H.119 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.98, B:D.118 Salt bridges: B:H.119 Water bridges: A:T.56 PO4.6: 4 residues within 4Å: Chain B: F.27, N.28, N.31, Y.32 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.28, B:N.31, B:Y.32, B:R.98 Water bridges: B:Y.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bianchini, F. et al., Human neutralizing antibodies to cold linear epitopes and subdomain 1 of the SARS-CoV-2 spike glycoprotein. Sci Immunol (2023)

Release Date

2022-12-21

Peptides

fp.006 light chain: A
fp.006 heavy chain: B
SARS-CoV-2 fusion peptide: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

fp.006 light chain

fp.006 heavy chain

SARS-CoV-2 fusion peptide

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