SMTL ID : 7sby.1

Structure of OC43 spike in complex with polyclonal Fab7 (Donor 269)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-3-mer

Ligands

13 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: 6 residues within 4Å: Chain C: N.342, E.346, N.371, S.374, T.616, Q.619 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain C: S.654, R.670, I.673, N.675 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: X.59 Chain D: R.147, I.149, K.204, N.206 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 7 residues within 4Å: Chain D: N.342, E.346, N.371, S.374, F.378, T.616, Q.619 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.378 NAG-NAG.6: 1 residues within 4Å: Chain D: N.713 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain D: D.727, N.738, T.740, A.741 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain D: V.1192, N.1193, M.1197 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain D: A.932, A.933, N.936 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain B: X.26 Chain D: V.136, N.137, N.171 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain E: D.727, N.738, T.740 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain E: I.149, K.204, R.205, N.206 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain E: N.371, S.374, T.616, Q.619 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain E: S.654, R.670, Y.672, I.673, N.675 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: 5 residues within 4Å: Chain C: R.147, I.149, L.162, K.204, N.206 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 2 residues within 4Å: Chain E: N.137, N.171 No protein-ligand interaction detected (PLIP)

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

NAG.16: 1 residues within 4Å: Chain C: N.137 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain C: N.212 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain C: A.448, N.449 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain C: N.713 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain C: D.727, N.738, T.740 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain C: S.785, N.787 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain C: A.932, A.933, N.936 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain C: V.1192, N.1193, M.1197, P.1206 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain C: N.695, Y.759 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain C: E.646, V.647, N.648 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain D: A.448, N.449 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain D: I.673, N.675 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain D: E.646, V.647, N.648 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain D: H.693, N.695, Y.759 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain D: S.785, V.786, N.787 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: K.1014 Chain D: V.1222, N.1223 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain E: A.932, A.933, N.936, G.940 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain E: L.62, N.63, Q.288 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain E: L.159, V.211, N.212 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain E: P.446, N.449 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain E: E.646, V.647, N.648 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain E: N.713 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain E: N.787 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain E: V.1192, N.1193, M.1197 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain E: V.1222, N.1223 Ligand excluded by PLIP

3 x 8Z9: Sapienic acid(Non-covalent)

8Z9.32: 16 residues within 4Å: Chain C: M.372, L.375, M.376, I.379, A.381, A.391, I.394, Y.395, I.402, L.441, L.603 Chain D: V.415, D.416, N.421, L.422, G.423 12 PLIP interactions: 4 interactions with chain D, 8 interactions with chain C Hydrophobic interactions: D:V.415, D:N.421, C:L.375, C:I.379, C:A.381, C:I.394, C:I.402, C:L.441, C:L.603 Hydrogen bonds: D:L.422, D:G.423, C:Y.395 8Z9.33: 17 residues within 4Å: Chain D: F.370, M.372, L.375, M.376, I.379, A.381, F.384, A.391, I.394, Y.395, L.603, L.605 Chain E: V.415, D.416, N.421, L.422, G.423 13 PLIP interactions: 9 interactions with chain D, 4 interactions with chain E Hydrophobic interactions: D:F.370, D:L.375, D:L.375, D:I.379, D:A.381, D:F.384, D:I.394, D:L.605, E:V.415 Hydrogen bonds: D:Y.395, E:N.421, E:L.422, E:G.423 8Z9.43: 12 residues within 4Å: Chain C: N.421, L.422, G.423 Chain E: F.370, M.372, L.375, A.391, Y.395, I.402, L.441, L.603, L.605 10 PLIP interactions: 7 interactions with chain E, 3 interactions with chain C Hydrophobic interactions: E:F.370, E:L.375, E:I.402, E:L.441, E:L.603, E:L.605, C:N.421 Hydrogen bonds: E:Y.395, C:L.422, C:G.423

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

Human polyclonal Fab model with polyalanine backbone - Heavy chain: AB
Spike protein: CDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
J

D
A

E
B

Human polyclonal Fab model with polyalanine backbone - Heavy chain

Spike protein

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