SMTL ID : 7nt9.1

Trimeric SARS-CoV-2 spike ectodomain in complex with biliverdin (closed conformation)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

30 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: 2 residues within 4Å: Chain A: Y.59, 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: 5 residues within 4Å: Chain A: N.153, T.155, V.158, K.160, V.202 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: E.163, N.196 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: T.139, N.265, T.267 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.139 NAG-NAG.6: 2 residues within 4Å: Chain A: N.647, W.664 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: N.748, L.953, Q.1102 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain A: N.832, Q.835 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain A: N.1129, H.1132, F.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain A: I.1163, N.1165 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain B: N.92 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain B: C.46, N.48, N.168 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 6 residues within 4Å: Chain B: N.153, T.155, N.156, V.158, K.160, V.202 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain B: E.163, N.196 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain B: T.139, N.265, T.267 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.139 NAG-NAG.16: 2 residues within 4Å: Chain B: N.647, W.664 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain B: N.748, Q.1102 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain B: N.832, Q.835 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain B: N.1129, H.1132, F.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 2 residues within 4Å: Chain B: I.1163, N.1165 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 2 residues within 4Å: Chain C: Y.59, N.92 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain C: C.46, N.48, N.168 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 6 residues within 4Å: Chain C: N.153, T.155, N.156, V.158, K.160, V.202 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 2 residues within 4Å: Chain C: E.163, N.196 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain C: T.139, N.265, T.267 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.139 NAG-NAG.26: 2 residues within 4Å: Chain C: N.647, W.664 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain C: N.748, L.953, Q.1102 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 2 residues within 4Å: Chain C: N.832, Q.835 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 3 residues within 4Å: Chain C: N.1129, H.1132, F.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 2 residues within 4Å: Chain C: I.1163, N.1165 No protein-ligand interaction detected (PLIP)

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

BLA.31: 10 residues within 4Å: Chain A: N.130, I.132, R.133, W.135, I.150, N.152, R.221, F.223, H.238, L.257 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:N.130, A:W.135, A:I.150, A:F.223, A:L.257 Hydrogen bonds: A:N.152, A:H.238 pi-Cation interactions: A:R.221, A:H.238 BLA.40: 10 residues within 4Å: Chain B: N.130, I.132, R.133, W.135, I.150, N.152, R.221, F.223, H.238, L.257 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.135, B:I.150, B:F.223, B:L.257 Hydrogen bonds: B:N.152, B:H.238 pi-Cation interactions: B:R.221, B:H.238 BLA.49: 11 residues within 4Å: Chain C: N.130, I.132, R.133, W.135, I.150, N.152, N.219, R.221, F.223, H.238, L.257 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:N.130, C:W.135, C:I.150, C:F.223, C:L.257 Hydrogen bonds: C:N.152, C:N.219 pi-Cation interactions: C:R.221, C:H.238

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

NAG.32: 4 residues within 4Å: Chain A: H.177, N.180, S.182, M.184 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain A: N.311, E.312, N.313 Chain B: K.589 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: N.362, Q.611 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: G.370, F.373, N.374 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain A: N.688 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain A: N.740, G.1162 Chain C: D.827 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain A: A.737, E.1103, N.1105 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain A: N.634 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain B: H.177, N.180, S.182, M.184 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain B: N.311, E.312, N.313 Chain C: K.589 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain B: N.362, Q.611 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain B: G.370, F.373, N.374 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain B: N.688 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain A: D.827 Chain B: N.740, G.1162 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain B: A.737, E.1103, N.1105 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain B: N.634 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain C: H.177, N.180, S.182, M.184 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain A: K.589 Chain C: N.311, E.312, N.313 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain C: N.362 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain C: G.370, F.373, N.374 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain C: N.688 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain B: D.827 Chain C: N.740, G.1162 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain C: A.737, E.1103, N.1105 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain C: N.634, T.635 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
A

B
B

C
C

Spike glycoprotein

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