SMTL ID : 7krr.1

Structural impact on SARS-CoV-2 spike protein by D614G substitution

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.50 Å

Oligo State

homo-trimer

Ligands

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

NAG-NAG.1: 2 residues within 4Å: Chain A: N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 8 residues within 4Å: Chain A: N.122, T.124, N.125, V.127, K.129, E.154, E.169, V.171 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.171 NAG-NAG.3: 2 residues within 4Å: Chain A: N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.616, T.618, Q.644 Chain B: Q.836 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.922 NAG-NAG.7: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain B: C.15, N.17 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 7 residues within 4Å: Chain B: N.122, A.123, T.124, N.125, V.127, E.169, V.171 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.171 NAG-NAG.13: 2 residues within 4Å: Chain B: N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 7 residues within 4Å: Chain A: R.457, K.458, K.462, E.465 Chain B: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain A: K.558 Chain B: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain B: N.616, T.618, Q.644 Chain C: I.834 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.922 NAG-NAG.18: 2 residues within 4Å: Chain B: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 2 residues within 4Å: Chain C: C.15, N.17 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 3 residues within 4Å: Chain C: N.331, P.579, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 3 residues within 4Å: Chain C: N.616, T.618, Q.644 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 4 residues within 4Å: Chain C: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922 NAG-NAG.26: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 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.8: 4 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.19: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.27: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP)

6 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.9: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.10: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.20: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.21: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.28: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.29: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.30: 1 residues within 4Å: Chain A: N.61 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: Y.144, K.147, N.149 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: G.232, N.234 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain A: N.331 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain A: F.338, G.339, N.343, L.368 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain A: N.709, I.1130, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain A: N.1158 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain B: K.147, N.149 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain B: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain B: N.343, F.374 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain B: N.709, N.710 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain B: N.1158 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.61 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain C: N.122, T.124, N.125, V.127 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain C: K.147, N.149 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: E.132, N.165 Ligand excluded by PLIP NAG.51: 5 residues within 4Å: Chain B: K.462, E.465 Chain C: T.108, N.234, T.236 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain C: N.280, N.282, T.284 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain C: N.343, V.367, L.368, S.371 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain A: D.796 Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain C: N.1158 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, J. et al., Structural impact on SARS-CoV-2 spike protein by D614G substitution. Science (2021)

Release Date

2021-03-24

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
A

Spike glycoprotein

Related Entries With Identical Sequence