SMTL ID : 8a94.1

SARS CoV2 Spike in the 2-up state in complex with Fab47.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

7 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG-NAG.1: 2 residues within 4Å: Chain A: Y.28, N.61 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: C.15, V.16, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: A.123, T.124, N.125, V.171 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.171 Hydrogen bonds: A:N.125 NAG-NAG.4: 3 residues within 4Å: Chain A: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain B: N.122, A.123, T.124, V.127, V.171 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.171 NAG-NAG.6: 2 residues within 4Å: Chain C: N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 9 residues within 4Å: Chain C: V.120, N.122, T.124, N.125, V.127, E.154, F.157, Y.160, V.171 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.160

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

NAG.8: 3 residues within 4Å: Chain A: E.281, N.282 Chain C: K.558 Ligand excluded by PLIP NAG.9: 5 residues within 4Å: Chain A: N.331, I.332, A.333, P.579, Q.580 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: T.716, N.717, Q.1071 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.1074 Chain B: Q.895 Ligand excluded by PLIP NAG.15: 5 residues within 4Å: Chain A: N.1098, G.1099, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: N.148, N.149, S.151, M.153 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: N.616, T.618, E.619 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: N.164, N.165 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.717, Q.1071 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.1074, T.1076 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.61 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain B: H.146, N.148, N.149, S.151, M.153 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: N.709, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.234 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.164, N.165 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: I.332, P.579, Q.580 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain B: K.558 Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: T.307, T.602, N.603 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.616, Q.644 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain A: D.796 Chain C: N.709, N.710, G.1131 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: N.717, Q.926, Q.1071 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain A: Q.895 Chain C: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.1134 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain C: H.146, N.148, N.149, S.151, M.153 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.331 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: G.339, N.343 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.165 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain C: G.232, I.233, N.234 Ligand excluded by PLIP NAG.50: 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

2023-05-03

Peptides

SARS-CoV2 Spike in 2-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
T

H
K

E
O

G
Q

I
E

SARS-CoV2 Spike in 2-up conformation in complex with Fab47

Fab47 (Heavy chain Variable domain)

Fab47 (Light chain Variable domain)

Related Entries With Identical Sequence