SMTL ID : 8oww.1

B5-5 nanobody bound to SARS-CoV-2 spike RBD (Wuhan)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 6 residues within 4Å: Chain A: F.9, G.10, F.13, N.14, L.39, S.42 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.14

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 8 residues within 4Å: Chain A: W.24, N.25, R.26, R.137 Chain B: Y.60, A.62, D.63, T.107 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.25, A:R.26, A:R.137, B:Y.60, B:T.107 EDO.3: 5 residues within 4Å: Chain A: P.97, D.98, D.99, P.134 Chain B: Y.56 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.98, A:D.98, A:D.99, A:D.99 EDO.4: 9 residues within 4Å: Chain A: P.97, D.99, F.100, T.101, F.135 Chain B: R.55, Y.56, P.103, Y.104 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:R.55 Hydrogen bonds: A:D.99, A:T.101 EDO.5: 5 residues within 4Å: Chain A: R.17, F.18, A.19, S.20, N.25 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.17

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: R.74, Y.124, Q.164, S.165, Y.166, G.167, N.172, Y.176 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.124, A:S.165 GOL.7: 10 residues within 4Å: Chain A: D.138, I.139, S.140 Chain B: Y.61, A.65, K.66, D.67, R.68, F.69, T.70 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.138, A:I.139, A:S.140, B:D.67

1 x NO3: NITRATE ION(Non-functional Binders)

NO3.8: 8 residues within 4Å: Chain B: V.3, S.28, L.30, Y.33, T.99, R.100, S.101, D.114 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.28, B:S.28, B:T.99, B:D.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cornish, K. et al., Structural and functional characterization of nanobodies that neutralize Omicron variants of SARS-CoV-2. Open Biology (2024)

Release Date

2024-05-08

Peptides

Spike protein S2': A
B5-5 nanobody: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Spike protein S2'

B5-5 nanobody