SMTL ID : 7ybl.1

SARS-CoV-2 B.1.620 variant spike (close state)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.60 Å

Oligo State

homo-trimer

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: 2 residues within 4Å: Chain A: C.15, N.17 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.164, N.165 Chain B: Y.348, I.465 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain A: N.613, T.615 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain B: C.15, N.17 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain B: E.130, N.164, N.165 Chain C: Y.348, I.465 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain B: N.613, T.615 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 2 residues within 4Å: Chain C: C.15, N.17 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain A: I.465 Chain C: N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 2 residues within 4Å: Chain C: N.613, T.615 No protein-ligand interaction detected (PLIP)

21 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.2: 5 residues within 4Å: Chain A: N.120, A.121, T.122, V.125, E.169 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.4: 8 residues within 4Å: Chain A: T.106, N.234, T.236 Chain B: K.455, S.456, N.457, L.458, K.459 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.456 NAG-NAG-MAN.5: 3 residues within 4Å: Chain A: N.277, E.278, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.7: 2 residues within 4Å: Chain A: N.714, Q.923 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.923 NAG-NAG-MAN.8: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.10: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.11: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.13: 5 residues within 4Å: Chain B: N.120, T.122, N.123, V.125, V.171 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.15: 9 residues within 4Å: Chain B: T.106, N.234, T.236 Chain C: R.454, K.455, S.456, N.457, L.458, K.459 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.16: 1 residues within 4Å: Chain B: N.279 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.18: 3 residues within 4Å: Chain B: N.714, L.919, Q.923 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.923 NAG-NAG-MAN.19: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.21: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.22: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.24: 5 residues within 4Å: Chain C: N.120, T.122, N.123, V.125, V.171 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.26: 9 residues within 4Å: Chain A: R.454, K.455, S.456, N.457, L.458, K.459 Chain C: T.106, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.27: 3 residues within 4Å: Chain C: N.277, E.278, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.29: 3 residues within 4Å: Chain C: N.714, L.919, Q.923 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Q.923 NAG-NAG-MAN.30: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.32: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.33: 1 residues within 4Å: Chain C: N.1131 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.9: 4 residues within 4Å: Chain A: A.703, E.1069, K.1070, N.1071 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.703 NAG-NAG-FUC.20: 3 residues within 4Å: Chain B: A.703, E.1069, N.1071 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.703 Hydrogen bonds: B:N.1071 NAG-NAG-FUC.31: 3 residues within 4Å: Chain C: A.703, E.1069, N.1071 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.703

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

NAG.34: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: N.328, Q.577, T.578 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain A: F.335, G.336, F.339, N.340, L.365 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain A: E.306, N.600 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain A: H.652, N.654 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain A: N.706, G.1128 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain A: N.1155 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain B: N.328, Q.577 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain B: F.335, G.336, F.339, N.340, L.365 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain B: N.600 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain B: H.652, N.654 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain A: D.793 Chain B: N.706 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain B: N.1155 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.49: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain C: N.328, P.576, Q.577 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain C: F.335, G.336, N.340 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain C: H.652, N.654 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain B: D.793 Chain C: N.706 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain C: N.1155 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xing, X. et al., Structures of SARS-CoV-2 spike protein alert noteworthy sites for the potential approaching variants. Virol Sin (2022)

Release Date

2023-08-09

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein