SMTL ID : 8a99.1

SARS Cov2 Spike in 1-up conformation complex with Fab47

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

8 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Non-functional Binders)

NAG-NAG.1: 2 residues within 4Å: Chain A: Y.28, N.61 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 1 residues within 4Å: Chain A: N.17 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.122, T.124, N.125, E.154 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NAG-NAG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain B: N.122, T.124, V.127, E.154, Y.160 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain C: N.122, N.125 No protein-ligand interaction detected (PLIP)

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

NAG.9: 3 residues within 4Å: Chain A: E.281, N.282 Chain C: K.558 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: N.709, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.717, Q.1071 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: A.706, N.1074 Chain B: Q.895 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: N.1098, G.1099, T.1100 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: H.146, N.148, N.149, S.151 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: N.616, T.618, E.619 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.165 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.1074, T.1076 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain B: H.146, N.148, N.149, S.151, M.153 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: N.709, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: G.232, I.233, N.234 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain A: K.462, F.464 Chain B: N.164, N.165 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: N.603, T.604 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: P.579, Q.580 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: N.801, S.803 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: E.281, N.282 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain A: D.796 Chain C: N.709, N.710, G.1131 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: N.717, Q.926, Q.1071 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.1134 Ligand excluded by PLIP NAG.46: 5 residues within 4Å: Chain C: H.146, N.148, N.149, S.151, M.153 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.331 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain C: N.343, S.371, S.373 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: N.164, N.165 Ligand excluded by PLIP NAG.51: 7 residues within 4Å: Chain B: W.353, R.355, P.463, F.464, E.465, R.466 Chain C: N.234 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pushparaj, P. et al., Immunoglobulin germline gene polymorphisms influence the function of SARS-CoV-2 neutralizing antibodies. Immunity (2023)

Release Date

2023-05-10

Peptides

SARS-CoV2 spike 1-up conformation in complex with Fab47: ABC
Fab47 (Heavy chain variable domain): DFH
Fab47 (Light chain Variable domain): EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
R

F
S

H
T

E
O

G
P

I
Q

SARS-CoV2 spike 1-up conformation in complex with Fab47

Fab47 (Heavy chain variable domain)

Fab47 (Light chain Variable domain)

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