SMTL ID : 7sbw.1

Structure of OC43 spike in complex with polyclonal Fab5 (Donor 1051)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-3-mer

Ligands

11 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.1: 6 residues within 4Å: Chain C: D.18, V.136, N.137, N.171, T.196, G.197 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 5 residues within 4Å: Chain C: E.346, N.371, S.374, F.378, T.616 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.378 NAG-NAG-BMA.5: 5 residues within 4Å: Chain C: F.726, D.727, N.738, T.740, A.741 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 5 residues within 4Å: Chain C: I.149, L.162, K.204, R.205, N.206 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 6 residues within 4Å: Chain D: 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-BMA.13: 1 residues within 4Å: Chain D: N.713 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 4 residues within 4Å: Chain D: A.932, A.933, N.936, G.940 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 4 residues within 4Å: Chain D: I.149, L.162, R.205, N.206 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 2 residues within 4Å: Chain D: P.446, N.449 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.24: 6 residues within 4Å: Chain E: N.342, E.346, N.371, S.374, F.378, T.616 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:F.378 NAG-NAG-BMA.29: 4 residues within 4Å: Chain E: I.149, L.162, R.205, N.206 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.3: 2 residues within 4Å: Chain C: A.448, N.449 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain C: N.713 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain C: A.932, A.933, N.936, G.940 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain C: V.1192, N.1193, M.1197 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: S.654, I.673, T.674, N.675 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain C: N.695, Y.759, S.760, K.761 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain D: N.137, T.196, G.197, V.198, V.199 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain D: F.726, D.727, N.738, T.740, A.741 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain D: V.1192, N.1193, M.1197 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain D: S.654, I.673, N.675 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain D: N.695, Y.759, S.760, K.761 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain C: K.1014 Chain D: V.1222, N.1223 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 4 residues within 4Å: Chain E: N.137, D.195, G.197, V.198 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain E: D.154, L.159, V.211, N.212 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.154 NAG-NAG.25: 1 residues within 4Å: Chain E: N.449 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 5 residues within 4Å: Chain E: F.726, D.727, N.738, T.740, A.741 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 4 residues within 4Å: Chain E: A.932, A.933, N.936, G.940 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 3 residues within 4Å: Chain E: V.1192, N.1193, M.1197 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 3 residues within 4Å: Chain E: S.654, I.673, N.675 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 4 residues within 4Å: Chain E: H.693, N.695, Y.759, K.761 No protein-ligand interaction detected (PLIP)

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

NAG.32: 3 residues within 4Å: Chain C: K.158, V.211, N.212 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.158 NAG.33: 2 residues within 4Å: Chain C: S.785, N.787 No protein-ligand interaction detected (PLIP) NAG.34: 3 residues within 4Å: Chain C: E.646, V.647, N.648 No protein-ligand interaction detected (PLIP) NAG.35: 2 residues within 4Å: Chain C: N.63, Q.288 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Q.288 NAG.36: 2 residues within 4Å: Chain D: K.158, N.212 No protein-ligand interaction detected (PLIP) NAG.37: 1 residues within 4Å: Chain D: N.787 No protein-ligand interaction detected (PLIP) NAG.38: 3 residues within 4Å: Chain D: E.646, V.647, N.648 No protein-ligand interaction detected (PLIP) NAG.39: 2 residues within 4Å: Chain D: N.63, Q.288 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Q.288 NAG.41: 2 residues within 4Å: Chain E: N.713, S.715 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.713, E:N.713 NAG.42: 1 residues within 4Å: Chain E: N.787 No protein-ligand interaction detected (PLIP) NAG.43: 3 residues within 4Å: Chain E: E.646, V.647, N.648 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:E.646 Hydrogen bonds: E:N.648 NAG.44: 2 residues within 4Å: Chain E: N.63, Q.288 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Q.288

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

8Z9.40: 15 residues within 4Å: Chain C: F.370, M.372, L.375, I.379, A.381, A.391, A.392, I.394, Y.395, I.402, L.603 Chain D: V.415, N.421, L.422, G.423 12 PLIP interactions: 9 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:F.370, C:L.375, C:L.375, C:I.379, C:A.381, C:I.394, C:I.402, C:L.603, D:V.415 Hydrogen bonds: C:Y.395, D:L.422, D:G.423 8Z9.45: 13 residues within 4Å: Chain C: N.421, L.422, G.423 Chain E: M.372, L.375, A.381, A.391, A.392, I.394, Y.395, I.402, L.603, L.605 10 PLIP interactions: 7 interactions with chain E, 3 interactions with chain C Hydrophobic interactions: E:L.375, E:A.381, E:I.394, E:I.402, E:L.603, E:L.605, C:N.421 Hydrogen bonds: E:Y.395, C:L.422, C:G.423 8Z9.46: 14 residues within 4Å: Chain D: M.372, L.375, M.376, A.391, A.392, I.394, Y.395, L.603, L.605 Chain E: V.415, D.416, N.421, L.422, G.423 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:L.375, D:I.394, D:L.605, E:V.415 Hydrogen bonds: D:Y.395, E:L.422, E: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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