SMTL ID : 7bbh.1

Structure of Coronavirus Spike from Smuggled Guangdong Pangolin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

12 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.164 Chain C: Y.347 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain A: N.233 Chain C: R.453, S.455, N.456, K.458, E.461 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.793, S.795, Q.796 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.1090, T.1092, H.1093, F.1095 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: Y.347 Chain B: N.164 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 7 residues within 4Å: Chain A: R.453, K.454, S.455, N.456, K.458, E.461 Chain B: N.233 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.793, S.795, Q.796 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: N.1090, T.1092, H.1093, F.1095 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain B: Y.347 Chain C: N.164 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 7 residues within 4Å: Chain B: R.453, K.454, S.455, N.456, K.458, E.461 Chain C: N.233 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain C: N.793, S.795, Q.796 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain C: N.1090, T.1092, H.1093, F.1095 No protein-ligand interaction detected (PLIP)

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

NAG.13: 4 residues within 4Å: Chain A: C.16, V.17, N.18, Y.137 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.31, Y.60, I.217 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: F.29, N.62 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: N.122, T.124, N.125, V.170 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.327, T.577 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.339 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: N.366 Chain C: F.452, Y.485, Q.489 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: N.701, G.1123 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.709, Q.1063 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.1126 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain A: N.612 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: N.112, Q.134, S.161 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: N.276, N.278 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain A: N.653 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: A.698, E.1064, N.1066 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: C.16, V.17, N.18, Y.137 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.31, Y.60, I.217 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: F.29, N.62 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain B: N.122, T.124, N.125, V.170 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.327, T.577 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.339 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain A: F.452, Y.485, Q.489 Chain B: N.366 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: N.701, G.1123 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: N.709, Q.1063 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain B: N.1126 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain B: N.612 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain B: N.112, Q.134, S.161 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain B: N.276, N.278 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain B: N.653 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain B: A.698, E.1064, N.1066 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain C: C.16, V.17, N.18, Y.137 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: N.31, Y.60, I.217 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: F.29, N.62 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain C: N.122, T.124, N.125, V.170 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: N.327, T.577 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.339 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain B: F.452, Y.485, Q.489 Chain C: N.366 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: N.701, G.1123 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain C: N.709, Q.1063 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain C: N.1126 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain C: N.612 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain C: N.112, Q.134, S.161 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain C: N.276, N.278 Ligand excluded by PLIP NAG.56: 1 residues within 4Å: Chain C: N.653 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain C: A.698, E.1064, N.1066 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wrobel, A.G. et al., Structure and binding properties of Pangolin-CoV spike glycoprotein inform the evolution of SARS-CoV-2. Nat Commun (2021)

Release Date

2020-12-30

Peptides

Surface glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Surface glycoprotein