SMTL ID : 8d5a.1

Middle state of SARS-CoV-2 BA.2 variant spike protein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

18 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.1: 5 residues within 4Å: Chain A: N.119, T.121, N.122, V.124, V.168 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.124, A:V.168 NAG-NAG-MAN.3: 2 residues within 4Å: Chain A: E.278, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.5: 4 residues within 4Å: Chain A: N.714, L.919, Q.923, Q.1068 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.919 NAG-NAG-MAN.6: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.8: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.9: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.10: 4 residues within 4Å: Chain B: N.119, T.121, N.122, V.124 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.13: 3 residues within 4Å: Chain A: K.555 Chain B: N.277, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.15: 3 residues within 4Å: Chain B: N.714, L.919, Q.1068 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.919 NAG-NAG-MAN.16: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.18: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.19: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.20: 6 residues within 4Å: Chain C: N.119, A.120, T.121, N.122, V.124, V.168 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.168 NAG-NAG-MAN.23: 4 residues within 4Å: Chain B: K.555 Chain C: N.277, E.278, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.25: 3 residues within 4Å: Chain C: N.714, L.919, Q.1068 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.919 NAG-NAG-MAN.26: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.28: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.29: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 5 residues within 4Å: Chain A: T.105, T.106, N.231, T.233, R.234 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.233 NAG-NAG.4: 4 residues within 4Å: Chain A: N.613, T.615, Q.641 Chain B: Q.833 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain A: Y.348, I.465 Chain B: E.129, N.161, N.162 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 7 residues within 4Å: Chain A: R.454, K.455, K.459, E.462 Chain B: T.105, N.231, T.233 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain B: N.613, T.615, Q.641 Chain C: Q.833 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain B: I.465 Chain C: E.129, N.161, N.162 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 5 residues within 4Å: Chain B: R.454, E.462 Chain C: T.105, N.231, T.233 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 3 residues within 4Å: Chain A: Q.833 Chain C: N.613, T.615 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.7: 3 residues within 4Å: Chain A: A.703, E.1069, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.17: 3 residues within 4Å: Chain B: A.703, E.1069, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.27: 2 residues within 4Å: Chain C: E.1069, N.1071 No protein-ligand interaction detected (PLIP)

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

NAG.30: 2 residues within 4Å: Chain A: Y.25, N.58 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain A: N.328, Q.577 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain A: D.336, N.340, F.368 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain A: N.600, T.601 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: Y.652, N.654 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: S.705, N.706 Chain B: Y.793 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain A: N.1155 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: Y.25, N.58 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain B: N.328, Q.577, T.578 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: N.340, F.368 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain B: N.600 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain B: Y.652, N.654 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain B: S.705, N.706 Chain C: Y.793 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain B: N.1155 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: Y.25, N.58 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.328 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: Y.652, N.654 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain A: Y.793 Chain C: N.706 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain C: N.1155 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, J. et al., Structural and functional characteristics of the SARS-CoV-2 Omicron subvariant BA.2 spike protein. Nat.Struct.Mol.Biol. (2023)

Release Date

2023-06-07

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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