SMTL ID : 7kdh.1

SARS-CoV-2 RBD up Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: N.122, T.124, N.125, V.127 Ligand excluded by PLIP NAG.2: 4 residues within 4Å: Chain A: T.108, N.234, T.236, R.237 Ligand excluded by PLIP NAG.3: 1 residues within 4Å: Chain A: N.282 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.5: 5 residues within 4Å: Chain A: F.338, G.339, F.342, N.343, L.368 Ligand excluded by PLIP NAG.6: 5 residues within 4Å: Chain A: E.309, K.310, G.601, N.603, T.604 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: N.709, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.10: 6 residues within 4Å: Chain A: N.717, F.718, T.719, Q.926, Q.1071 Ligands: NAG.11 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Ligands: NAG.10 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain A: N.801, S.803, Q.804 Ligands: NAG.13 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Ligands: NAG.12 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.1074 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: N.1098, T.1100, F.1103 Ligands: NAG.16 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Ligands: NAG.15 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: I.1132, N.1134 Ligands: NAG.18 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Ligands: NAG.17 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain B: V.120, N.122, A.123, V.127 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: T.108, N.234 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: N.717, Q.926, Q.1071 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.1074 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: G.339, F.342, N.343 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Ligands: NAG.36 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: I.1132, N.1134 Ligands: NAG.30 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Ligands: NAG.28 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: E.132, N.165 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain B: N.801, S.803, Q.804 Ligands: NAG.34 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: Q.804 Ligands: NAG.32 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: N.709, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain B: N.1098, T.1100, F.1103 Ligands: NAG.27 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: Y.421, R.454, Q.493 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: A.706, N.1074 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Ligands: NAG.54 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: G.232, N.234 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain C: N.122, T.124, V.127, V.171 Ligand excluded by PLIP NAG.46: 6 residues within 4Å: Chain C: N.717, F.718, T.719, Q.926, Q.1071 Ligands: NAG.51 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: N.280, N.282 Ligand excluded by PLIP NAG.48: 5 residues within 4Å: Chain C: F.338, G.339, F.342, N.343, L.368 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain C: S.112, C.131, E.132, N.165 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Ligands: NAG.46 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Ligands: NAG.58 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain C: N.1134 Ligands: NAG.41 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain C: Q.804, F.817 Ligands: NAG.56 Ligand excluded by PLIP NAG.56: 4 residues within 4Å: Chain C: N.801, S.803, Q.804 Ligands: NAG.55 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain C: N.616, T.618 Ligand excluded by PLIP NAG.58: 4 residues within 4Å: Chain C: N.1098, T.1100, F.1103 Ligands: NAG.53 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gobeil, S.M. et al., D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. Cell Rep (2021)

Release Date

2020-11-04

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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