SMTL ID : 7uap.1

Structure of the SARS-CoV-2 S 6P trimer in complex with the neutralizing antibody Fab fragment, C1520

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-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)

NAG-NAG.1: 5 residues within 4Å: Chain A: N.122, V.127, E.154, F.157, V.171 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: H.146, N.148, N.149, S.151, M.153 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: T.108, N.234, T.236 Chain B: N.460, K.462 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.1095, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain B: N.122, T.124, N.125, V.127 Chain F: N.74 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: H.146, K.147, N.148, N.149 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: N.234 Chain C: K.458, K.462, E.465 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: N.1095, G.1096, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 6 residues within 4Å: Chain C: N.122, T.124, N.125, V.127, E.154 Chain H: S.30 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain C: H.146, N.148, N.149 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain C: T.108, N.234 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain C: N.1095, H.1098, F.1100 No protein-ligand interaction detected (PLIP)

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

NAG.13: 3 residues within 4Å: Chain A: F.59, N.61, P.631 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.165 Chain B: Y.351 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: E.281, N.282 Chain B: K.557, K.558 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: G.339, N.343, S.371 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: N.616, T.618, E.619, Q.644 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: N.706, G.1128 Chain C: D.793 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: N.714, L.919, Q.923 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.798, S.800 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: E.1069, K.1070, N.1071 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: C.1079, I.1129, N.1131 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: Y.28, T.29, N.30, N.61 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.164, N.165 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: E.281, N.282 Chain C: K.558 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: F.342, N.343, V.367, A.372 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain A: D.793 Chain B: N.706, G.1128 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain B: N.714, L.919, Q.923, Q.1068 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.1131 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: Y.28, F.59, N.61 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: K.113, N.164, N.165 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.282 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain C: N.331, T.333, N.334, Q.580 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain C: G.339, N.343, S.371, A.372 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: N.616, T.618, E.619 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain B: D.793 Chain C: N.706, G.1128 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain C: N.714, L.919, Q.923, Q.1068 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.798, S.800 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: A.703, N.1071 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain C: N.1131 Ligand excluded by PLIP NAG.45: 5 residues within 4Å: Chain E: S.17, V.18, N.19, S.69, T.78 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain G: N.19, F.76 Ligand excluded by PLIP NAG.47: 13 residues within 4Å: Chain I: N.19, L.47, S.49, L.50, H.56, T.57, K.58, G.59, I.62, F.66, S.67, G.68, L.77 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Z. et al., Analysis of memory B cells identifies conserved neutralizing epitopes on the N-terminal domain of variant SARS-Cov-2 spike proteins. Immunity (2022)

Release Date

2022-04-27

Peptides

Spike glycoprotein: ABC
C1520 Fab Heavy Chain: DFH
C1520 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

C1520 Fab Heavy Chain

C1520 Fab Light Chain

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