SMTL ID : 9uxe.1

SARS-CoV2 Spike protein with Fab fragment antibody KXD355,state2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.17 Å

Oligo State

hetero-3-3-3-mer

Ligands

3 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.1: 8 residues within 4Å: Chain C: G.339, N.343 Chain H: G.31, R.53, F.103, G.104, V.105, I.107 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:I.107, H:F.103 Hydrogen bonds: H:F.103 NAG-NAG-BMA-FUC.7: 8 residues within 4Å: Chain A: G.339, F.342, N.343, L.368 Chain D: F.103, G.104, V.105, I.107 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.103 NAG-NAG-BMA-FUC.13: 10 residues within 4Å: Chain B: F.338, G.339, F.342, N.343 Chain F: G.31, R.53, F.103, G.104, V.105, I.107 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:F.103

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.2: 3 residues within 4Å: Chain C: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain C: N.717, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain A: T.108, N.234, T.236 Chain B: E.465 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.236 NAG-NAG.9: 4 residues within 4Å: Chain A: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain A: N.1098, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain B: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.922 NAG-NAG.16: 4 residues within 4Å: Chain B: K.795, N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.19: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: N.280, E.281, N.282 Chain B: K.558 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.331 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: E.309, N.603 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: A.706, N.1074 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain A: S.112, K.113, E.132, N.164, N.165 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain B: N.122, A.123, T.124, N.125 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: N.280, E.281, N.282 Chain C: K.558 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.331 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain B: N.1074 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain B: S.112, E.132, N.164, N.165 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain C: N.331, P.579, Q.580, L.582 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: T.307, N.603 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.616, Q.644 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.45: 5 residues within 4Å: Chain B: Q.895 Chain C: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, X. et al., A rare B cell clonotype imprinted by ancestral SARS-CoV-2 develops cross-sarbecovirus neutralization in immune recalls. Cell Rep (2025)

Release Date

2025-07-16

Peptides

Spike glycoprotein: ABC
Antibody KXD355, heavy chain: DFH
Antibody KXD355, light chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

F
H

H
J

E
E

G
L

I
K

Spike glycoprotein

Antibody KXD355, heavy chain

Antibody KXD355, light chain

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