SMTL ID : 7cwm.1

Complex of SARS-CoV-2 spike protein and Fab P17 with one RBD in open state and two RBD in closed state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

14 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: 5 residues within 4Å: Chain A: T.108, N.234, T.236 Chain C: R.457, E.465 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.457 NAG-NAG.2: 3 residues within 4Å: Chain A: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: I.1132, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.1098, G.1099, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain B: I.1132, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain C: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 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.12: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: N.1098, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain C: I.1132, V.1133, N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.15: 2 residues within 4Å: Chain A: N.603, T.604 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: H.655, V.656, N.657 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: N.709, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.61 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: N.603, T.604 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: H.655, V.656, N.657 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: N.709, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: H.655, V.656, N.657 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: D.796 Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yao, H. et al., Rational development of a human antibody cocktail that deploys multiple functions to confer Pan-SARS-CoVs protection. Cell Res. (2021)

Release Date

2020-12-16

Peptides

Spike glycoprotein: ABC
P17 heavy chain: DEF
P17 light chain: GHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
G

E
H

F
I

G
L

H
J

I
K

Spike glycoprotein

P17 heavy chain

P17 light chain

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