SMTL ID : 7k8t.1

Structure of the SARS-CoV-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, C002 (State 2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

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.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 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.3: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 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: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain B: N.234 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain C: N.234 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain C: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.16: 1 residues within 4Å: Chain A: N.61 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.122, N.125 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: N.280, E.281, N.282, T.284 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.343 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain A: N.165 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.61 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain B: N.122, N.125, V.127, K.129 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain B: N.280, E.281, N.282, T.284 Chain C: K.558 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain B: Y.380, G.381, V.382, S.383 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.616, Q.644 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.709, G.1131 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain B: N.165 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.61 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain C: N.122, N.125, V.127, K.129 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.39: 7 residues within 4Å: Chain A: F.486 Chain C: V.367, L.368, S.371, F.374 Chain I: S.31, Y.32 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: H.655, V.656, N.657 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.165 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barnes, C.O. et al., SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies. Nature (2020)

Release Date

2020-10-21

Peptides

Spike glycoprotein: ABC
C002 Fab Heavy Chain: DFH
C002 Fab Light Chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
M

H
O

E
L

G
N

I
P

Spike glycoprotein

C002 Fab Heavy Chain

C002 Fab Light Chain

Related Entries With Identical Sequence