SMTL ID : 7v82.1

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 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

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

NAG-NAG.1: 3 residues within 4Å: Chain A: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: N.331, P.579, Q.580, T.581, L.582 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: F.338, G.339, F.342, N.343 No protein-ligand interaction detected (PLIP) 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, L.922 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 No protein-ligand interaction detected (PLIP) 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: 6 residues within 4Å: Chain B: N.122, T.124, N.125, V.127, E.154, V.171 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.171 NAG-NAG.12: 2 residues within 4Å: Chain B: E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain B: N.331, P.579, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain B: N.616, T.618, Q.644 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain B: N.709 Chain C: D.796 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain B: N.717 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain B: S.704, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain B: N.1098, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 2 residues within 4Å: Chain C: E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 4 residues within 4Å: Chain C: N.331, Q.580, T.581, L.582 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.581 NAG-NAG.23: 3 residues within 4Å: Chain C: N.616, T.618, Q.644 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 3 residues within 4Å: Chain A: D.796 Chain C: N.709, G.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 1 residues within 4Å: Chain C: N.717 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain C: S.704, A.706, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 3 residues within 4Å: Chain C: N.1098, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP)

26 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.30: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain A: V.120, N.122, T.124, N.125 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: N.164, N.165 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain A: G.232, N.234 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain A: N.20, T.22, W.258, A.260, G.261 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain A: K.187, N.188, H.207 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: N.164, N.165 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain B: N.234 Ligand excluded by PLIP NAG.41: 5 residues within 4Å: Chain B: F.338, F.342, N.343, S.371, F.374 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain B: N.603, T.604 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain B: N.20, T.22, Q.23, W.258, G.261 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain B: L.176, N.188, H.207 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain C: Y.28, T.29, N.61 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain C: N.122, T.124, N.125 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: 2 residues within 4Å: Chain C: G.339, N.343 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain C: Y.655, N.657 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain C: N.20, T.22, W.258, G.261 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain C: K.187, N.188, H.207, P.209 Ligand excluded by PLIP NAG.55: 5 residues within 4Å: Chain E: N.53, T.55, E.57, N.58, Q.340 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 1. 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
E

E
D

F
F

Spike glycoprotein

Angiotensin-converting enzyme 2,Green fluorescent protein

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