SMTL ID : 8cy7.1

SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-34

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

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

NAG-NAG.1: 2 residues within 4Å: Chain A: I.1132, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 7 residues within 4Å: Chain A: S.112, K.113, Q.115, E.132, N.165, T.167 Chain B: F.464 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: N.1098, G.1099, H.1101, F.1103 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.1101 NAG-NAG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain C: N.343, S.373, L.441 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain C: N.1098, G.1099, H.1101, F.1103 No protein-ligand interaction detected (PLIP)

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

NAG.13: 7 residues within 4Å: Chain A: Y.28, F.59, S.60, N.61, L.629, T.630, P.631 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: V.171, S.172 Ligand excluded by PLIP NAG.15: 6 residues within 4Å: Chain A: N.331, I.332, S.530, T.531, N.532, Q.580 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: E.309, N.603, T.604 Ligand excluded by PLIP NAG.17: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: N.709, N.710, I.1130, G.1131 Ligand excluded by PLIP NAG.20: 6 residues within 4Å: Chain A: A.706, A.713, E.1072, K.1073, N.1074 Chain C: Q.895 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: N.717, T.719, L.922, Q.1071 Ligand excluded by PLIP NAG.22: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: K.795, N.801, S.803, Q.804 Ligand excluded by PLIP NAG.24: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: N.148, N.149, W.152 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain A: N.234 Ligand excluded by PLIP NAG.27: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: G.339, N.343 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Ligands: NAG.36 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain B: Y.28, S.60, N.61, T.630, P.631 Ligand excluded by PLIP NAG.31: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain B: N.331, P.579, Q.580, T.581, L.582 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.603, T.604 Ligand excluded by PLIP NAG.34: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: H.655, V.656, N.657 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Ligands: NAG.29 Ligand excluded by PLIP NAG.37: 6 residues within 4Å: Chain A: Q.895 Chain B: A.706, A.713, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.38: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain B: F.342, N.343, F.374 Ligand excluded by PLIP NAG.40: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain B: N.280, E.281, N.282 Chain C: K.558 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain B: G.199, N.234 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain B: T.114, Q.115, N.164, N.165 Chain C: F.464 Ligand excluded by PLIP NAG.44: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: T.345 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain C: Y.28, T.29, N.61, T.630 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Ligands: NAG.55 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain A: K.558 Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain C: N.331, I.332, S.530, Q.580 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain C: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.53: 7 residues within 4Å: Chain B: L.894, Q.895 Chain C: A.706, A.713, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.54: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Ligands: NAG.47 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain C: N.148, N.149, W.152 Ligand excluded by PLIP NAG.57: 5 residues within 4Å: Chain A: F.464, E.465 Chain C: E.132, N.164, N.165 Ligand excluded by PLIP NAG.58: 3 residues within 4Å: Chain C: T.108, N.234, T.236 Ligand excluded by PLIP NAG.59: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.60: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.61: 1 residues within 4Å: Ligands: NAG.62 Ligand excluded by PLIP NAG.62: 1 residues within 4Å: Ligands: NAG.61 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiang, Y. et al., Superimmunity by pan-sarbecovirus nanobodies. Cell Rep (2022)

Release Date

2022-07-06

Peptides

Spike glycoprotein: ABC
pan-sarbecovirus nanobody 2-38: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Spike glycoprotein

pan-sarbecovirus nanobody 2-38

Related Entries With Identical Sequence