SMTL ID : 7v83.1

Cryo-EM structure of SARS-CoV-2 S-Gamma variant (P.1) in complex with Angiotensin-converting enzyme 2 (ACE2) ectodomain, three ACE2-bound form conformation 2

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

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: 3 residues within 4Å: Chain A: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: F.338, G.339, N.343, V.367 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.367 NAG-NAG.4: 2 residues within 4Å: Chain A: N.616, T.618 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: N.709 Chain B: D.796 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain A: N.717, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: S.704, A.706, N.1074 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.706 NAG-NAG.9: 3 residues within 4Å: Chain A: N.1098, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain B: N.122, A.123, T.124, N.125, V.127 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain B: N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain B: E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain B: N.331, P.579, Q.580, L.582 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain B: N.616, T.618 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain B: N.709 Chain C: D.796 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 1 residues within 4Å: Chain B: N.717 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain B: S.704, A.706, N.1074 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.706 NAG-NAG.20: 3 residues within 4Å: Chain B: N.1098, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 2 residues within 4Å: Chain C: E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain C: N.331, P.579, Q.580, L.582 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 2 residues within 4Å: Chain C: N.616, T.618 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain A: D.796 Chain C: N.709, G.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 2 residues within 4Å: Chain C: N.717, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 3 residues within 4Å: Chain C: S.704, A.706, N.1074 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.706 NAG-NAG.29: 3 residues within 4Å: Chain C: N.1098, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.31: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain A: N.122, T.124, N.125, V.127 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain A: N.164, N.165 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain A: G.232, I.233, N.234 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain A: Y.655, N.657 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain A: N.20, T.22, W.258, A.260 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain A: K.187, N.188 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain B: Y.28, F.59, N.61 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain B: N.234 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain B: F.342, N.343, L.368 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain B: Y.655, N.657 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain B: N.20, T.22, W.258, A.260 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain B: L.176, N.188, H.207, P.209 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain C: Y.28, F.59, S.60, N.61 Ligand excluded by PLIP NAG.47: 5 residues within 4Å: Chain C: N.122, A.123, T.124, N.125, V.127 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: E.132, N.165 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain C: G.232, I.233, N.234 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain C: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain C: N.188 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain D: N.53, T.55, Q.340 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain D: N.90, L.91 Ligand excluded by PLIP NAG.56: 4 residues within 4Å: Chain D: N.103, S.106, V.107, A.193 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain D: N.322 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain D: D.431, N.432 Ligand excluded by PLIP NAG.59: 5 residues within 4Å: Chain D: H.417, S.420, D.543, S.545, N.546 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, T.J. et al., Cryo-EM structure of SARS-CoV-2 S-Gamma variant (P.1) in complex with Angiotensin-converting enzyme 2 (ACE2) ectodomain, three ACE2-bound form conformation 2. To Be Published

Release Date

2021-10-06

Peptides

Spike glycoprotein: ABC
Angiotensin-converting enzyme 2,Green fluorescent protein: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Spike glycoprotein

Angiotensin-converting enzyme 2,Green fluorescent protein

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