SMTL ID : 7wgb.1

Neutral Omicron Spike Trimer in complex with ACE2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-mer

Ligands

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

NAG-NAG.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: P.327, N.328, Q.577 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.577 NAG-NAG.3: 2 residues within 4Å: Chain A: N.714, Q.923 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: A.703, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.231 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain B: N.714, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain B: S.708, N.1071 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.1071 NAG-NAG.11: 2 residues within 4Å: Chain B: N.798, S.800 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain B: N.328, Q.577, L.579 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain A: R.454, K.455, S.456 Chain C: N.231 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain C: N.328, T.330 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain C: N.714, L.919 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain C: A.703, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP)

5 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.6: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 2 residues within 4Å: Chain B: I.1129, N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 3 residues within 4Å: Chain C: N.1095, H.1098, F.1100 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.1098 NAG-NAG-BMA.21: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP)

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

NAG.22: 2 residues within 4Å: Chain A: V.16, S.253 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: C.15, N.17, N.135 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain A: D.336, F.339, N.340, L.365, L.368 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain A: N.600 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain A: N.654 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain A: N.613, C.614, Q.641 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain A: N.706 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: N.120, A.121, T.122, N.123 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.143, S.251 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain B: C.15, N.17, C.134, N.135 Ligand excluded by PLIP NAG.33: 6 residues within 4Å: Chain B: Y.377, G.378, A.408, P.409, F.426, T.427 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: N.600, T.601 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain B: N.654 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: N.613, T.615, Q.641 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain B: N.706 Ligand excluded by PLIP NAG.39: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: S.251 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: N.17, T.19, N.135 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain C: F.335, D.336, F.339, N.340 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: Y.652, V.653, N.654 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain C: N.613, C.614, Q.641 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain B: Y.793 Chain C: N.706 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain D: K.398, S.402, N.528 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain D: N.72, L.73 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain D: E.294, N.304, M.305, W.310 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain D: T.34, N.35, Q.322 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain E: H.399, S.402, S.527, N.528 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain E: N.72 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain E: V.298, N.304 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain E: T.34, N.35, E.39 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cui, Z. et al., Structural and functional characterizations of infectivity and immune evasion of SARS-CoV-2 Omicron. Cell (2022)

Release Date

2022-06-22

Peptides

Spike glycoprotein: ABC
Processed angiotensin-converting enzyme 2: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
F

Spike glycoprotein

Processed angiotensin-converting enzyme 2

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