SMTL ID : 7l2c.2 (1 other biounit)

Crystallographic structure of neutralizing antibody 2-51 in complex with SARS-CoV-2 spike N-terminal domain (NTD)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.65 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: N.17 Ligands: CA.11 No protein-ligand interaction detected (PLIP) NAG.2: 1 residues within 4Å: Chain A: N.61 No protein-ligand interaction detected (PLIP) NAG.3: 2 residues within 4Å: Chain A: G.232, N.234 No protein-ligand interaction detected (PLIP) NAG.4: 3 residues within 4Å: Chain A: Q.115, E.132, N.165 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.165 Water bridges: A:Q.115 NAG.5: 2 residues within 4Å: Chain A: N.148, N.149 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.148, A:N.148 NAG.6: 1 residues within 4Å: Chain A: N.282 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.282 NAG.7: 5 residues within 4Å: Chain A: N.122, T.124, V.127, E.154 Ligands: CA.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.154 Hydrogen bonds: A:T.124, A:T.124

16 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.8: 2 residues within 4Å: Chain A: D.198, Y.200 No protein-ligand interaction detected (PLIP) CA.9: 2 residues within 4Å: Chain A: T.167, I.231 No protein-ligand interaction detected (PLIP) CA.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.11: 1 residues within 4Å: Ligands: NAG.1 No protein-ligand interaction detected (PLIP) CA.12: 1 residues within 4Å: Chain A: Y.28 No protein-ligand interaction detected (PLIP) CA.13: 2 residues within 4Å: Chain A: E.156 Ligands: NAG.7 No protein-ligand interaction detected (PLIP) CA.18: 1 residues within 4Å: Chain B: Y.184 No protein-ligand interaction detected (PLIP) CA.19: 1 residues within 4Å: Chain B: V.11 No protein-ligand interaction detected (PLIP) CA.20: 1 residues within 4Å: Chain B: L.45 No protein-ligand interaction detected (PLIP) CA.21: 1 residues within 4Å: Chain B: D.55 No protein-ligand interaction detected (PLIP) CA.22: 3 residues within 4Å: Chain B: M.70, T.71, E.72 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.72 CA.23: 1 residues within 4Å: Chain B: N.212 No protein-ligand interaction detected (PLIP) CA.24: 1 residues within 4Å: Chain B: E.220 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.220 CA.27: 2 residues within 4Å: Chain B: L.178 Chain C: E.163 No protein-ligand interaction detected (PLIP) CA.28: 1 residues within 4Å: Chain C: A.82 No protein-ligand interaction detected (PLIP) CA.29: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

ACT.14: 5 residues within 4Å: Chain A: Q.14, R.158, R.246 Chain B: G.26, T.28 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.158, A:R.246 ACT.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ACT.16: 1 residues within 4Å: Chain A: H.245 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.245 ACT.25: 1 residues within 4Å: Chain B: G.114 No protein-ligand interaction detected (PLIP) ACT.26: 5 residues within 4Å: Chain B: R.38, Q.39, A.40, G.44, E.46 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.40 Hydrogen bonds: B:A.40 ACT.30: 6 residues within 4Å: Chain C: Q.39, H.41, K.47, F.64, E.83, D.84 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.64 Hydrogen bonds: C:Q.39, C:H.41 Salt bridges: C:K.47

1 x CAC: CACODYLATE ION(Non-covalent)

CAC.17: 6 residues within 4Å: Chain A: V.83, L.110, F.135, C.136, N.137, Q.239 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.239

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cerutti, G. et al., Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite. Cell Host Microbe (2021)

Release Date

2021-02-10

Peptides

Spike glycoprotein: A
2-51 heavy chain: B
2-51 light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Spike glycoprotein

2-51 heavy chain

2-51 light chain

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