SMTL ID : 7yr3.1

SARS-CoV-2 BA.2.75 S Trimer in complex with ACE2(state2)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.52 Å

Oligo State

hetero-3-2-mer

Ligands

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

NAG-NAG.1: 2 residues within 4Å: Chain A: N.714, L.919 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 1 residues within 4Å: Chain A: N.798 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: A.703, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain B: N.714, L.919 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain B: N.798 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain B: A.703, 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: 1 residues within 4Å: Chain D: N.1071 No protein-ligand interaction detected (PLIP)

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

NAG.10: 4 residues within 4Å: Chain A: Y.25, N.58, S.254, W.255 Ligand excluded by PLIP NAG.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain A: S.152, L.154, V.156, Y.157 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: Y.141, N.146, K.147 Ligand excluded by PLIP NAG.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: K.110 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: N.279, T.281 Chain D: K.555 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.328, Q.577 Ligand excluded by PLIP NAG.18: 14 residues within 4Å: Chain A: S.405, Q.406, A.408, P.409, G.410, Q.411, T.412, G.413, N.414, I.415, A.416, D.417, K.421, L.422 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.600 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.613 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.654 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: N.706 Chain B: Y.793 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.1131 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain B: Y.25, N.58, S.254, W.255 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.71 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: S.152, L.154, Y.157 Ligand excluded by PLIP NAG.28: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.29: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.30: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain A: K.555 Chain B: N.279 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.328, I.329 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: K.437, L.438 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.600 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: N.613, T.615 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: Y.652, N.654 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: N.706 Chain D: Y.793 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain B: N.1095, T.1097, H.1098 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain B: N.1131 Ligand excluded by PLIP NAG.40: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.41: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: S.402, D.525, N.528 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.72 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: N.304, M.305 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain C: N.35, T.37, E.39, N.40 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain D: Y.25, N.58 Ligand excluded by PLIP NAG.49: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain D: L.154, Y.157 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain D: Y.141, R.149 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain B: K.555 Chain D: N.279 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain D: N.328, I.329, N.331, L.332 Ligand excluded by PLIP NAG.54: 8 residues within 4Å: Chain D: Q.406, A.408, Q.411, T.412, G.413, A.416, D.417, K.421 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain D: N.600 Ligand excluded by PLIP NAG.56: 1 residues within 4Å: Chain D: N.613 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain D: Y.652, N.654 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain A: 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 NAG.63: 3 residues within 4Å: Chain E: S.402, S.527, N.528 Ligand excluded by PLIP NAG.64: 2 residues within 4Å: Chain E: N.72, T.74 Ligand excluded by PLIP NAG.65: 1 residues within 4Å: Chain E: N.304 Ligand excluded by PLIP NAG.66: 4 residues within 4Å: Chain E: N.35, T.37, E.39, Q.322 Ligand excluded by PLIP

2 x ZN: ZINC ION(Non-covalent)

ZN.42: 2 residues within 4Å: Chain C: H.356, H.360 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.356, C:H.360, C:H.360 ZN.61: 3 residues within 4Å: Chain E: H.356, H.360, E.384 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:H.356, E:H.360

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

CL.43: 4 residues within 4Å: Chain C: R.151, W.459, D.481, P.482 Ligand excluded by PLIP CL.62: 4 residues within 4Å: Chain E: W.147, R.151, W.460, D.481 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

Spike glycoprotein: ABD
Angiotensin-converting enzyme 2: CE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

D
F

C
D

E
G

Spike glycoprotein

Angiotensin-converting enzyme 2

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