SMTL ID : 8wmf.1

Structure of the SARS-CoV-2 EG.5.1 spike glycoprotein (closed-1 state)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

15 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: N.712, L.917 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.917 NAG-NAG.2: 2 residues within 4Å: Chain A: N.796, S.798 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1093, T.1095, H.1096, F.1098 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 6 residues within 4Å: Chain B: N.712, L.917 Chain D: N.712, L.917 Ligands: NAG-NAG.46, NAG-NAG.46 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.917 NAG-NAG.17: 6 residues within 4Å: Chain B: N.796, S.798 Chain D: N.796, S.798 Ligands: NAG-NAG.47, NAG-NAG.47 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 10 residues within 4Å: Chain B: N.1093, T.1095, H.1096, F.1098 Chain D: N.1093, T.1095, H.1096, F.1098 Ligands: NAG-NAG.48, NAG-NAG.48 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.1096 NAG-NAG.31: 6 residues within 4Å: Chain C: N.712, L.917 Chain E: N.712, L.917 Ligands: NAG-NAG.61, NAG-NAG.61 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.917 NAG-NAG.32: 6 residues within 4Å: Chain C: N.796, S.798 Chain E: N.796, S.798 Ligands: NAG-NAG.62, NAG-NAG.62 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 10 residues within 4Å: Chain C: N.1093, T.1095, H.1096, F.1098 Chain E: N.1093, T.1095, H.1096, F.1098 Ligands: NAG-NAG.63, NAG-NAG.63 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:H.1096 NAG-NAG.46: 6 residues within 4Å: Chain B: N.712, L.917 Chain D: N.712, L.917 Ligands: NAG-NAG.16, NAG-NAG.16 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.917 NAG-NAG.47: 6 residues within 4Å: Chain B: N.796, S.798 Chain D: N.796, S.798 Ligands: NAG-NAG.17, NAG-NAG.17 No protein-ligand interaction detected (PLIP) NAG-NAG.48: 10 residues within 4Å: Chain B: N.1093, T.1095, H.1096, F.1098 Chain D: N.1093, T.1095, H.1096, F.1098 Ligands: NAG-NAG.18, NAG-NAG.18 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.1096 NAG-NAG.61: 6 residues within 4Å: Chain C: N.712, L.917 Chain E: N.712, L.917 Ligands: NAG-NAG.31, NAG-NAG.31 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.917 NAG-NAG.62: 6 residues within 4Å: Chain C: N.796, S.798 Chain E: N.796, S.798 Ligands: NAG-NAG.32, NAG-NAG.32 No protein-ligand interaction detected (PLIP) NAG-NAG.63: 10 residues within 4Å: Chain C: N.1093, T.1095, H.1096, F.1098 Chain E: N.1093, T.1095, H.1096, F.1098 Ligands: NAG-NAG.33, NAG-NAG.33 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:H.1096

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

NAG.4: 1 residues within 4Å: Chain A: N.57 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: N.118, T.120, V.123 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: N.159, N.160 Ligand excluded by PLIP NAG.7: 11 residues within 4Å: Chain A: T.104, N.229, T.231 Chain C: R.452, S.454, K.455, K.457 Chain E: R.452, S.454, K.455, K.457 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: E.276, N.277 Chain C: K.553 Chain E: K.553 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: N.326, Q.575 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: H.334, N.338, F.366 Ligand excluded by PLIP NAG.11: 5 residues within 4Å: Chain A: N.611, T.613, Q.639 Chain B: I.829 Chain D: I.829 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.652 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: Y.702, S.703, N.704 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: E.1067, N.1069 Chain B: Q.890 Chain D: Q.890 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.1129 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: N.57 Chain D: N.57 Ligands: NAG.49 Ligand excluded by PLIP NAG.20: 7 residues within 4Å: Chain B: N.118, T.120, V.123 Chain D: N.118, T.120, V.123 Ligands: NAG.50 Ligand excluded by PLIP NAG.21: 5 residues within 4Å: Chain B: N.159, N.160 Chain D: N.159, N.160 Ligands: NAG.51 Ligand excluded by PLIP NAG.22: 11 residues within 4Å: Chain A: R.452, S.454, K.455, K.457 Chain B: T.104, N.229, T.231 Chain D: T.104, N.229, T.231 Ligands: NAG.52 Ligand excluded by PLIP NAG.23: 6 residues within 4Å: Chain A: K.553 Chain B: E.276, N.277 Chain D: E.276, N.277 Ligands: NAG.53 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain B: N.326, Q.575 Chain D: N.326, Q.575 Ligands: NAG.54 Ligand excluded by PLIP NAG.25: 7 residues within 4Å: Chain B: H.334, N.338, F.366 Chain D: H.334, N.338, F.366 Ligands: NAG.55 Ligand excluded by PLIP NAG.26: 9 residues within 4Å: Chain B: N.611, T.613, Q.639 Chain C: I.829 Chain D: N.611, T.613, Q.639 Chain E: I.829 Ligands: NAG.56 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.652 Chain D: N.652 Ligands: NAG.57 Ligand excluded by PLIP NAG.28: 7 residues within 4Å: Chain B: Y.702, S.703, N.704 Chain D: Y.702, S.703, N.704 Ligands: NAG.58 Ligand excluded by PLIP NAG.29: 7 residues within 4Å: Chain B: E.1067, N.1069 Chain C: Q.890 Chain D: E.1067, N.1069 Chain E: Q.890 Ligands: NAG.59 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: N.1129 Chain D: N.1129 Ligands: NAG.60 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: N.57 Chain E: N.57 Ligands: NAG.64 Ligand excluded by PLIP NAG.35: 7 residues within 4Å: Chain C: N.118, T.120, V.123 Chain E: N.118, T.120, V.123 Ligands: NAG.65 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain C: N.159, N.160 Chain E: N.159, N.160 Ligands: NAG.66 Ligand excluded by PLIP NAG.37: 15 residues within 4Å: Chain B: R.452, S.454, K.455, K.457 Chain C: T.104, N.229, T.231 Chain D: R.452, S.454, K.455, K.457 Chain E: T.104, N.229, T.231 Ligands: NAG.67 Ligand excluded by PLIP NAG.38: 7 residues within 4Å: Chain B: K.553 Chain C: E.276, N.277 Chain D: K.553 Chain E: E.276, N.277 Ligands: NAG.68 Ligand excluded by PLIP NAG.39: 5 residues within 4Å: Chain C: N.326, Q.575 Chain E: N.326, Q.575 Ligands: NAG.69 Ligand excluded by PLIP NAG.40: 7 residues within 4Å: Chain C: H.334, N.338, F.366 Chain E: H.334, N.338, F.366 Ligands: NAG.70 Ligand excluded by PLIP NAG.41: 8 residues within 4Å: Chain A: I.829 Chain C: N.611, T.613, Q.639 Chain E: N.611, T.613, Q.639 Ligands: NAG.71 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: N.652 Chain E: N.652 Ligands: NAG.72 Ligand excluded by PLIP NAG.43: 7 residues within 4Å: Chain C: Y.702, S.703, N.704 Chain E: Y.702, S.703, N.704 Ligands: NAG.73 Ligand excluded by PLIP NAG.44: 6 residues within 4Å: Chain A: Q.890 Chain C: E.1067, N.1069 Chain E: E.1067, N.1069 Ligands: NAG.74 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: N.1129 Chain E: N.1129 Ligands: NAG.75 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain B: N.57 Chain D: N.57 Ligands: NAG.19 Ligand excluded by PLIP NAG.50: 7 residues within 4Å: Chain B: N.118, T.120, V.123 Chain D: N.118, T.120, V.123 Ligands: NAG.20 Ligand excluded by PLIP NAG.51: 5 residues within 4Å: Chain B: N.159, N.160 Chain D: N.159, N.160 Ligands: NAG.21 Ligand excluded by PLIP NAG.52: 11 residues within 4Å: Chain A: R.452, S.454, K.455, K.457 Chain B: T.104, N.229, T.231 Chain D: T.104, N.229, T.231 Ligands: NAG.22 Ligand excluded by PLIP NAG.53: 6 residues within 4Å: Chain A: K.553 Chain B: E.276, N.277 Chain D: E.276, N.277 Ligands: NAG.23 Ligand excluded by PLIP NAG.54: 5 residues within 4Å: Chain B: N.326, Q.575 Chain D: N.326, Q.575 Ligands: NAG.24 Ligand excluded by PLIP NAG.55: 7 residues within 4Å: Chain B: H.334, N.338, F.366 Chain D: H.334, N.338, F.366 Ligands: NAG.25 Ligand excluded by PLIP NAG.56: 9 residues within 4Å: Chain B: N.611, T.613, Q.639 Chain C: I.829 Chain D: N.611, T.613, Q.639 Chain E: I.829 Ligands: NAG.26 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain B: N.652 Chain D: N.652 Ligands: NAG.27 Ligand excluded by PLIP NAG.58: 7 residues within 4Å: Chain B: Y.702, S.703, N.704 Chain D: Y.702, S.703, N.704 Ligands: NAG.28 Ligand excluded by PLIP NAG.59: 7 residues within 4Å: Chain B: E.1067, N.1069 Chain C: Q.890 Chain D: E.1067, N.1069 Chain E: Q.890 Ligands: NAG.29 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain B: N.1129 Chain D: N.1129 Ligands: NAG.30 Ligand excluded by PLIP NAG.64: 3 residues within 4Å: Chain C: N.57 Chain E: N.57 Ligands: NAG.34 Ligand excluded by PLIP NAG.65: 7 residues within 4Å: Chain C: N.118, T.120, V.123 Chain E: N.118, T.120, V.123 Ligands: NAG.35 Ligand excluded by PLIP NAG.66: 5 residues within 4Å: Chain C: N.159, N.160 Chain E: N.159, N.160 Ligands: NAG.36 Ligand excluded by PLIP NAG.67: 15 residues within 4Å: Chain B: R.452, S.454, K.455, K.457 Chain C: T.104, N.229, T.231 Chain D: R.452, S.454, K.455, K.457 Chain E: T.104, N.229, T.231 Ligands: NAG.37 Ligand excluded by PLIP NAG.68: 7 residues within 4Å: Chain B: K.553 Chain C: E.276, N.277 Chain D: K.553 Chain E: E.276, N.277 Ligands: NAG.38 Ligand excluded by PLIP NAG.69: 5 residues within 4Å: Chain C: N.326, Q.575 Chain E: N.326, Q.575 Ligands: NAG.39 Ligand excluded by PLIP NAG.70: 7 residues within 4Å: Chain C: H.334, N.338, F.366 Chain E: H.334, N.338, F.366 Ligands: NAG.40 Ligand excluded by PLIP NAG.71: 8 residues within 4Å: Chain A: I.829 Chain C: N.611, T.613, Q.639 Chain E: N.611, T.613, Q.639 Ligands: NAG.41 Ligand excluded by PLIP NAG.72: 3 residues within 4Å: Chain C: N.652 Chain E: N.652 Ligands: NAG.42 Ligand excluded by PLIP NAG.73: 7 residues within 4Å: Chain C: Y.702, S.703, N.704 Chain E: Y.702, S.703, N.704 Ligands: NAG.43 Ligand excluded by PLIP NAG.74: 6 residues within 4Å: Chain A: Q.890 Chain C: E.1067, N.1069 Chain E: E.1067, N.1069 Ligands: NAG.44 Ligand excluded by PLIP NAG.75: 3 residues within 4Å: Chain C: N.1129 Chain E: N.1129 Ligands: NAG.45 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nomai, T. et al., Virological characteristics of the SARS-CoV-2 Omicron EG.5.1 variant. Biorxiv (2024)

Release Date

2024-04-24

Peptides

Spike glycoprotein: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

Spike glycoprotein

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