SMTL ID : 7yr2.1

SARS-CoV-2 BA.2.75 S Trimer in complex with ACE2(state1)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.30 Å

Oligo State

hetero-1-3-mer

Ligands

9 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 B: N.714, L.919, Q.923 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain B: N.798, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain B: A.703, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain C: N.714, L.919 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain C: N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain D: N.714, L.919 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain D: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain D: A.703, N.1071 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.10: 4 residues within 4Å: Chain A: H.356, E.357, H.360, E.384 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.356, A:H.360, A:E.384, A:E.384

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 4 residues within 4Å: Chain A: R.151, W.459, W.460, K.463 Ligand excluded by PLIP

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

NAG.12: 2 residues within 4Å: Chain A: S.527, N.528 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.72 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: K.291, N.304 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: N.35, T.37, E.39, Q.322 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain B: Y.25, F.56, S.57, N.58 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: T.70, N.71 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain B: N.119, A.120, N.122, Y.157 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.146, R.149 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.162 Ligand excluded by PLIP NAG.21: 5 residues within 4Å: Chain B: T.111, N.231, T.233 Chain D: R.463, D.464 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.279 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.328, Q.577 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: N.340, A.341, L.438 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.600 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.613, T.615 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.654 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.706 Chain C: I.791, Y.793 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.1095, T.1097, H.1098 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.1131 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: F.56, N.58 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.71 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: N.119, N.122, V.124 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.146 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.161, N.162 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain C: T.105, T.111, N.231, I.232 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.279 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.328 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: H.336, N.340 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: N.613, T.615 Chain D: Q.833 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.654 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.706 Chain D: Y.793 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.1131 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain D: Y.25, N.58 Ligand excluded by PLIP NAG.47: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain D: N.119, N.122 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain D: N.146 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain D: N.161, N.162 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain C: R.463 Chain D: T.105, T.111, N.231 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain D: N.279 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain D: N.328 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain D: N.340 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain D: N.600 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain B: I.831, Q.833 Chain D: N.613 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain D: N.654 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain B: Y.793 Chain D: N.706 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain D: N.1095, T.1097, H.1098 Ligand excluded by PLIP NAG.60: 1 residues within 4Å: Chain D: N.1131 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, Y. et al., Characterization of the enhanced infectivity and antibody evasion of Omicron BA.2.75. Cell Host Microbe (2022)

Release Date

2022-10-19

Peptides

Angiotensin-converting enzyme 2: A
Spike glycoprotein: BCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
E

D
C

Angiotensin-converting enzyme 2

Spike glycoprotein

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