SMTL ID : 7b62.1

Crystal structure of SARS-CoV-2 spike protein N-terminal domain in complex with biliverdin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

monomer

Ligands

1 x BLA: BILIVERDINE IX ALPHA(Non-covalent)

BLA.1: 13 residues within 4Å: Chain A: I.101, R.102, G.103, W.104, N.121, V.126, M.177, R.190, F.192, H.207, L.226 Ligands: PEG.11, PGE.14 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.104, A:F.192, A:L.226, A:L.226 Hydrogen bonds: A:N.121, A:H.207, A:H.207 Water bridges: A:N.188, A:R.190, A:R.190 pi-Cation interactions: A:H.207

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

NAG.2: 3 residues within 4Å: Chain A: C.15, N.17, N.137 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.17 Water bridges: A:N.17 NAG.3: 2 residues within 4Å: Chain A: Y.28, N.61 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.61 NAG.4: 6 residues within 4Å: Chain A: N.122, T.124, N.125, V.127, K.129, V.171 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.124 Hydrogen bonds: A:T.124, A:K.129, A:K.129 Water bridges: A:N.122, A:N.122, A:N.122 NAG.5: 4 residues within 4Å: Chain A: H.146, N.149, S.151, M.153 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.149, A:S.151, A:S.151 Water bridges: A:H.146 NAG.6: 3 residues within 4Å: Chain A: Q.115, E.132, N.165 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.115 Water bridges: A:N.165, A:N.165 NAG.7: 2 residues within 4Å: Chain A: G.232, N.234 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.234 Water bridges: A:N.234 NAG.8: 3 residues within 4Å: Chain A: N.280, E.281, N.282 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.281 Water bridges: A:N.282, A:N.282, A:T.284

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.9: 7 residues within 4Å: Chain A: Y.38, D.40, K.41, V.42, N.282, G.283, T.284 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.284 Water bridges: A:N.282 PG4.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

PEG.11: 3 residues within 4Å: Chain A: F.175 Ligands: BLA.1, PGE.14 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.176 PEG.12: 4 residues within 4Å: Chain A: K.41, P.225, L.226, V.227 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.41, A:D.228 Water bridges: A:D.228 PEG.13: 5 residues within 4Å: Chain A: Y.170, V.171, S.172, Q.173, P.174 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.171, A:Q.173

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.14: 6 residues within 4Å: Chain A: V.126, Y.170, S.172, Q.173 Ligands: BLA.1, PEG.11 No protein-ligand interaction detected (PLIP) PGE.15: 4 residues within 4Å: Chain A: Q.14, F.157, Y.160, S.161 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.14 PGE.16: 5 residues within 4Å: Chain A: D.198, G.199, P.230, I.231, G.232 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.232

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.17: 1 residues within 4Å: Chain A: F.43 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rosa, A. et al., SARS-CoV-2 can recruit a heme metabolite to evade antibody immunity. Sci Adv (2021)

Release Date

2021-04-28

Peptides

Spike glycoprotein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Spike glycoprotein