SMTL ID : 8asy.1

SARS-CoV-2 Omicron BA.2.75 RBD in complex with ACE2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

hetero-1-1-mer

Ligands

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: E.220, E.465, G.587, W.588, T.590 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.220, A:W.588 GOL.3: 4 residues within 4Å: Chain A: G.301, G.533, Q.534, F.537 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.533, A:Q.534 GOL.9: 5 residues within 4Å: Chain A: Q.80, H.177, Y.178, E.190, R.201 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.80, A:H.177, A:Y.178, A:E.190, A:R.201, A:R.201 GOL.11: 6 residues within 4Å: Chain A: Q.84, Y.178, Y.184, W.185, G.187, D.188 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.178, A:W.185, A:G.187 GOL.12: 5 residues within 4Å: Chain A: F.22, D.332, G.334, F.372, R.375 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.375 GOL.13: 5 residues within 4Å: Chain A: F.22, S.25, S.26, S.29, W.51 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.26, A:W.51 GOL.14: 2 residues within 4Å: Chain A: E.132, N.136 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.132, A:E.132, A:N.136 GOL.15: 7 residues within 4Å: Chain A: I.273, P.397, E.412, T.416, E.417, F.420, H.522 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.416, A:T.416, A:E.417 GOL.17: 6 residues within 4Å: Chain A: K.457, W.460, E.471, P.474, H.475, Y.595 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.457, A:H.475, A:H.475 GOL.18: 9 residues within 4Å: Chain A: K.295, F.296, S.299, H.399, S.402, I.403, S.527, N.528 Ligands: NAG.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.402 GOL.19: 5 residues within 4Å: Chain A: T.9 Chain B: Y.89, F.124, R.125, Y.141 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.89, B:R.125, B:R.125, B:Y.141 GOL.20: 1 residues within 4Å: Chain B: G.150 No protein-ligand interaction detected (PLIP)

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

NAG.2: 4 residues within 4Å: Chain A: N.304, M.305, T.306, Q.307 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.304 NAG.4: 5 residues within 4Å: Chain A: K.398, S.402, D.525, N.528 Ligands: GOL.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.402, A:S.402, A:N.528 NAG.5: 3 residues within 4Å: Chain A: F.267, N.414, W.576 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.267 Hydrogen bonds: A:N.414 NAG.6: 3 residues within 4Å: Chain A: N.35, T.37, Q.322 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.35 NAG.7: 3 residues within 4Å: Chain A: K.8, N.72, V.75 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.8 NAG.8: 6 residues within 4Å: Chain A: Q.63, Q.83, N.85, V.89, N.176, H.177 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.83 Hydrogen bonds: A:N.85, A:N.85

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

CL.10: 4 residues within 4Å: Chain A: R.151, W.459, W.460, D.481 Ligand excluded by PLIP

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.16: 9 residues within 4Å: Chain A: A.135, N.136, S.137, L.138, R.143, N.259, L.260, Y.261, S.262 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.261, A:S.262, A:S.262

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huo, J. et al., A delicate balance between antibody evasion and ACE2 affinity for Omicron BA.2.75. Cell Rep (2022)

Release Date

2023-01-11

Peptides

Processed angiotensin-converting enzyme 2: A
Spike protein S1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Processed angiotensin-converting enzyme 2

Spike protein S1

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