SMTL ID : 7f5g.1 (1 other biounit)

The crystal structure of RBD-Nanobody complex, DL4 (SA4)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- FUC- NAG- FUC: alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUC-NAG-FUC.1: 5 residues within 4Å: Chain A: G.13, N.17, V.41, L.42, S.45 No protein-ligand interaction detected (PLIP)

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: F.16, N.17, A.46, W.110 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.17 GOL.3: 4 residues within 4Å: Chain A: P.100, D.102, F.138 Ligands: ACT.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.102 Water bridges: A:T.104, A:T.104 GOL.4: 5 residues within 4Å: Chain A: Y.43, N.44, A.46, S.47, F.48 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.44, A:A.46, A:F.48, A:F.48 Water bridges: A:N.44 GOL.5: 2 residues within 4Å: Chain A: S.57, T.59 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.57, A:T.59 GOL.6: 4 residues within 4Å: Chain A: G.150, S.151, T.152, N.161 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.151, A:T.152, A:T.152, A:N.161 GOL.7: 5 residues within 4Å: Chain A: E.80, Q.83, G.90, K.91 Ligands: ACT.13 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.80, A:Q.83, A:K.91, A:K.91, A:K.91 GOL.15: 3 residues within 4Å: Chain A: T.144, I.146, F.164 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.144, A:T.144 Water bridges: A:E.158 GOL.16: 2 residues within 4Å: Chain B: G.13, G.14 1 PLIP interactions: 1 interactions with chain B Water bridges: B:L.15

8 x ACT: ACETATE ION(Non-functional Binders)

ACT.8: 3 residues within 4Å: Chain A: R.20, F.21, A.22 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.28 Salt bridges: A:R.20 ACT.9: 3 residues within 4Å: Chain A: Y.25, L.126 Chain B: H.60 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.126 Hydrogen bonds: A:Y.25 Salt bridges: B:H.60 ACT.10: 6 residues within 4Å: Chain A: R.29, Y.70, F.138, S.188, E.190 Ligands: GOL.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.188 Salt bridges: A:R.29 ACT.11: 5 residues within 4Å: Chain A: S.40, Y.43, N.44, P.58, T.59 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.43 Water bridges: A:S.40 ACT.12: 2 residues within 4Å: Chain A: N.113, N.114 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.113 Water bridges: A:N.114, A:Q.180 ACT.13: 5 residues within 4Å: Chain A: R.82, Q.83, Q.88, T.89 Ligands: GOL.7 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.83, A:Q.83, A:T.89 ACT.14: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.29 ACT.17: 2 residues within 4Å: Chain B: R.61, Y.63 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.61 Water bridges: B:R.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, T. et al., Isolation, characterization, and structure-based engineering of a neutralizing nanobody against SARS-CoV-2. Int.J.Biol.Macromol. (2022)

Release Date

2022-05-25

Peptides

Spike glycoprotein: A
Nanobody DL4: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Spike glycoprotein

Nanobody DL4

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