SMTL ID : 9dhy.1

Structure of SARS-CoV-2 spike in complex with antibody Fab COVIC-154

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

9 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: 4 residues within 4Å: Chain C: N.721, L.926, Q.930, Q.1075 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: N.54 Chain C: D.800, N.805, S.807, Q.808 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain C: N.1138 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain F: N.721, L.926, Q.930, Q.1075 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain D: N.54 Chain F: D.800, N.805, S.807, Q.808 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain F: N.1138 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain I: N.721, L.926, Q.930, Q.1075 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain G: N.54 Chain I: D.800, N.805, S.807, Q.808 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain I: N.1138 No protein-ligand interaction detected (PLIP)

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

NAG.10: 3 residues within 4Å: Chain C: N.284, E.285, N.286 Ligand excluded by PLIP NAG.11: 5 residues within 4Å: Chain C: F.342, G.343, F.346, N.347, L.372 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain C: N.620, T.622, Q.648 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain C: N.713, G.1135 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain C: N.1078, F.1079, T.1080 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain C: N.1102, G.1103, H.1105, F.1107 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain C: N.335, Q.584 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain F: N.284, E.285, N.286 Ligand excluded by PLIP NAG.18: 5 residues within 4Å: Chain F: F.342, G.343, F.346, N.347, L.372 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain F: N.620, T.622, Q.648 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain F: N.713, G.1135 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain F: N.1078, F.1079, T.1080 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain F: N.1102, G.1103, H.1105, F.1107 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain F: N.335, Q.584 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain I: N.284, E.285, N.286 Ligand excluded by PLIP NAG.25: 5 residues within 4Å: Chain I: F.342, G.343, F.346, N.347, L.372 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain I: N.620, T.622, Q.648 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain I: N.713, G.1135 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain I: N.1078, F.1079, T.1080 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain I: N.1102, G.1103, H.1105, F.1107 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain I: N.335, Q.584 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schendel, S.L. et al., A global collaboration for systematic analysis of broad-ranging antibodies against the SARS-CoV-2 spike protein. Cell Rep (2025)

Release Date

2025-04-16

Peptides

Antibody Fab COVIC-154 Heavy Chain: ADG
Antibody Fab COVIC-154 Light Chain: BEH
Spike glycoprotein: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

G
I

B
B

E
E

H
J

C
C

F
F

I
K

Antibody Fab COVIC-154 Heavy Chain

Antibody Fab COVIC-154 Light Chain

Spike glycoprotein