SMTL ID : 7sb5.1

Structure of OC43 spike in complex with polyclonal Fab3 (Donor 1412)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-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 A: F.726, D.727, N.738, T.740 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.342, N.371, S.374, T.616 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: N.137, T.138, Q.169, N.171 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain B: F.726, D.727, N.738, T.740, A.741 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.741 NAG-NAG.6: 3 residues within 4Å: Chain B: V.1192, N.1193, M.1197 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain C: L.19, N.137, Q.169, N.171 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: E.346, N.371, S.374 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain C: F.726, D.727, N.738, T.740, A.741 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain C: R.147, E.164, N.206 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 4 residues within 4Å: Chain A: R.147, K.204, R.205, N.206 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 5 residues within 4Å: Chain B: R.147, L.162, K.204, R.205, N.206 No protein-ligand interaction detected (PLIP)

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

NAG.12: 3 residues within 4Å: Chain A: N.137, Q.169, N.171 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.212 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.713 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: A.932, N.935, N.936, G.940 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: V.1192, N.1193, M.1197 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: S.654, I.673, T.674, N.675 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: N.695, Y.759, S.760, K.761 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: E.646, V.647, N.648 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: K.352, A.448, N.449 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: V.1222, N.1223 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.787 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: L.159, N.212 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: P.446, N.449 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: F.712, N.713 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: V.786, N.787, Q.800 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain B: A.932, N.936, G.940, A.941, E.942 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: S.654, R.670, I.673, N.675 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: H.693, N.695, K.761 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.648 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain B: N.342, N.371, S.374, T.616 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: V.1222, N.1223 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.212 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: A.448, N.449 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.713 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.787 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: A.932, A.933, N.936 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: V.1192, N.1193, M.1197 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: I.673, N.675 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: H.693, N.695, Y.759 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: V.647, N.648 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain B: D.892, Q.1013 Chain C: N.1223 Ligand excluded by PLIP

3 x PLM: PALMITIC ACID(Non-covalent)

PLM.33: 14 residues within 4Å: Chain A: F.370, M.372, L.375, M.376, I.379, F.384, A.391, Y.395, I.402, L.603, L.605 Chain B: N.421, L.422, G.423 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.370, A:L.375, A:L.375, A:I.379, A:I.379, A:F.384, A:I.402, A:L.603, A:L.605, B:N.421 Hydrogen bonds: A:Y.395, B:L.422, B:G.423 PLM.34: 14 residues within 4Å: Chain B: M.372, L.375, M.376, I.379, A.391, A.392, Y.395, L.441, L.603 Chain C: V.415, D.416, N.421, L.422, G.423 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:L.375, B:M.376, B:L.441, B:L.441, B:L.603, C:V.415, C:N.421 Hydrogen bonds: B:Y.395, C:L.422, C:G.423 PLM.45: 15 residues within 4Å: Chain A: D.416, G.420, N.421, L.422, G.423 Chain C: F.370, M.372, L.375, M.376, A.391, A.392, I.394, Y.395, I.402, L.603 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:N.421, C:F.370, C:L.375, C:I.402, C:L.603 Hydrogen bonds: A:L.422, A:G.423, C:Y.395

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bangaru, S. et al., Structural mapping of antibody landscapes to human betacoronavirus spike proteins. Sci Adv (2022)

Release Date

2022-05-04

Peptides

Spike protein: ABC
Human polyclonal Fab model with polyalanine backbone - Heavy chain: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
B

C
A

D
H

E
L

Spike protein

Human polyclonal Fab model with polyalanine backbone - Heavy chain

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