SMTL ID : 7nkt.1

RBD domain of SARS-CoV2 in complex with neutralizing nanobody NM1226

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: G.21, N.25, L.50 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.50 Hydrogen bonds: A:N.25

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

PO4.2: 5 residues within 4Å: Chain A: R.85, E.88, Q.91, K.99, I.100 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.88, A:Q.91, A:K.99 Salt bridges: A:R.85

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

PEG.3: 4 residues within 4Å: Chain B: E.45, G.46, A.60, F.107 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.45, B:G.46 PEG.4: 2 residues within 4Å: Chain B: R.44, W.115 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.44 Water bridges: B:R.44 PEG.5: 5 residues within 4Å: Chain A: V.185 Chain B: R.44, F.107, V.108, A.109 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.44, B:A.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wagner, T.R. et al., NeutrobodyPlex-monitoring SARS-CoV-2 neutralizing immune responses using nanobodies. Embo Rep. (2021)

Release Date

2021-05-12

Peptides

Spike protein S1: A
neutralizing nanobody NM1226: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

Spike protein S1

neutralizing nanobody NM1226

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