SMTL ID : 7ntc.1

Trimeric SARS-CoV-2 spike ectodomain bound to P008_056 Fab

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-mer

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: 4 residues within 4Å: Chain A: C.46, V.47, N.48, N.168 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain A: N.153, T.155, N.156, V.158, E.185, V.202 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: E.163, N.196 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: T.139, N.265 Chain B: E.496 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.647, C.648, W.664 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain A: N.748, Q.957 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: N.832, S.834, Q.835 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain A: N.1129, T.1131, H.1132, 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: N.48, N.168 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 6 residues within 4Å: Chain B: V.151, N.153, V.158, E.185, Y.191, V.202 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain B: E.163, N.196 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain B: T.139, N.265, T.267 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.139, B:T.267 Hydrogen bonds: B:T.267 NAG-NAG.14: 1 residues within 4Å: Chain B: N.647 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain B: N.748, L.953 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain B: N.832, S.834 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain B: N.1129, H.1132, F.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 1 residues within 4Å: Chain B: N.1165 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 6 residues within 4Å: Chain C: N.153, T.155, N.156, V.158, S.186, V.202 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.156 NAG-NAG.20: 3 residues within 4Å: Chain C: E.163, N.195, N.196 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 1 residues within 4Å: Chain C: N.647 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 2 residues within 4Å: Chain C: N.748, Q.957 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 2 residues within 4Å: Chain C: N.832, Q.835 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain C: N.1129, T.1131, H.1132, F.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain C: I.1163, V.1164, N.1165 No protein-ligand interaction detected (PLIP)

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

BLA.26: 10 residues within 4Å: Chain A: N.130, I.132, W.135, I.150, N.152, R.221, F.223, I.234, H.238, L.257 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.132, A:W.135, A:I.150, A:F.223, A:I.234, A:L.257, A:L.257 Hydrogen bonds: A:N.152 Salt bridges: A:R.221 pi-Cation interactions: A:R.221, A:H.238 BLA.36: 6 residues within 4Å: Chain B: N.130, R.133, M.208, R.221, F.223, L.257 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:N.130, B:L.257 pi-Cation interactions: B:R.221, B:H.238

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

NAG.27: 2 residues within 4Å: Chain A: N.179, N.180 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain A: E.312, N.313 Chain B: K.589 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: N.362, I.363, Q.611 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain A: G.370, F.373, N.374, L.399 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain A: N.688, N.689 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain A: N.740, G.1162 Chain C: D.827 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain A: A.737, N.1105 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain A: Y.59, N.61, N.92 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain A: N.634 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: H.177, N.180 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain B: E.312, N.313 Chain C: K.589 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain B: N.362, P.610, Q.611 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain B: G.370, F.373, N.374 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain B: H.686, N.688 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain B: N.740, I.1161 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain B: N.1105 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain B: Y.59, N.92 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain B: N.634 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: N.179, N.180 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: E.312, N.313 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.362 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain C: G.370, F.373, 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, I.1161 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain C: E.1103, N.1105 Ligand excluded by PLIP NAG.53: 5 residues within 4Å: Chain C: Y.59, T.60, N.61, S.91, N.92 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain C: C.46, N.48 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain C: N.265 Ligand excluded by PLIP NAG.56: 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
P008_056 Fab Heavy chain: D
P008_056 Fab Light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
L

Spike glycoprotein

P008_056 Fab Heavy chain

P008_056 Fab Light chain

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