SMTL ID : 7nta.1

Trimeric SARS-CoV-2 spike ectodomain in complex with biliverdin (one RBD erect)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

25 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: Y.59, N.61, N.92 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: C.46, N.48, N.168 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.196 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: N.265 Chain B: E.496 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.647, W.664, R.665 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.664 NAG-NAG.6: 3 residues within 4Å: Chain A: N.748, L.953, Q.1102 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.953 NAG-NAG.7: 2 residues within 4Å: Chain A: N.832, S.834 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: N.1129, T.1131, F.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain A: N.1165 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain B: Y.59, N.92 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 6 residues within 4Å: Chain B: N.153, T.155, V.158, K.160, E.185, V.202 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.202 Hydrogen bonds: B:K.160, B:K.160 NAG-NAG.12: 3 residues within 4Å: Chain B: G.263, I.264, N.265 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain B: N.647, W.664 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain B: N.748, L.953 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.953 NAG-NAG.15: 2 residues within 4Å: Chain B: N.832, S.834 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain B: N.1129, H.1132, F.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 1 residues within 4Å: Chain B: N.1165 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain C: Y.59, N.92 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain C: N.153, T.155, V.158, V.202 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain C: T.139, N.265, T.267 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.267 NAG-NAG.21: 2 residues within 4Å: Chain C: N.647, W.664 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 1 residues within 4Å: Chain C: N.748 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 3 residues within 4Å: Chain C: N.832, S.834, Q.835 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 2 residues within 4Å: Chain C: N.1129, F.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 1 residues within 4Å: Chain C: N.1165 No protein-ligand interaction detected (PLIP)

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

BLA.26: 12 residues within 4Å: Chain A: N.130, I.132, R.133, G.134, W.135, I.150, N.152, M.208, R.221, F.223, H.238, L.257 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.135, A:I.150, A:F.223, A:L.257, A:L.257 Hydrogen bonds: A:N.152, A:H.238, A:H.238 pi-Cation interactions: A:R.221, A:H.238 BLA.34: 13 residues within 4Å: Chain B: N.130, I.132, R.133, W.135, I.150, N.152, M.208, N.219, R.221, F.223, I.234, H.238, L.257 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.135, B:I.150, B:F.223, B:I.234, B:L.257, B:L.257 Hydrogen bonds: B:N.152, B:N.219 pi-Stacking: B:H.238 pi-Cation interactions: B:R.221 BLA.45: 11 residues within 4Å: Chain C: E.127, I.132, R.133, W.135, I.150, N.152, M.208, R.221, F.223, H.238, L.257 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:W.135, C:W.135, C:I.150, C:F.223, C:L.257 Hydrogen bonds: C:N.152, C:R.221 pi-Cation interactions: C:H.238

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

NAG.27: 3 residues within 4Å: Chain A: N.311, E.312, N.313 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain A: N.362 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain A: N.374 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain A: N.688 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain A: N.740 Chain C: D.827 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: E.1103, N.1105 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain A: N.634 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain B: H.177, N.179, N.180, M.184 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: E.312, N.313 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: N.362, Q.611 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: N.374, A.403 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: H.686, N.688 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain A: D.827 Chain B: N.740, G.1162 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain B: A.737, E.1103, N.1105 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain B: C.46, N.48, N.168 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain B: N.196 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain B: N.634, T.635 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain C: H.177, N.179, N.180 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain A: K.589 Chain C: E.312, N.313 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: N.362, Q.611 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain C: N.374 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain C: N.688 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain C: N.740, G.1162 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain C: A.737, E.1103, N.1105 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain C: C.46, N.48 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain C: N.196 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain C: N.634 Ligand excluded by 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: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
A

Spike glycoprotein

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