SMTL ID : 7sbx.1

Structure of OC43 spike in complex with polyclonal Fab6 (Donor 1051)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-mer

Ligands

17 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: 3 residues within 4Å: Chain A: N.137, N.171, T.196 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: E.346, N.371, S.374, T.616, Q.619 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: F.726, D.727, N.738, T.740, A.741 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: V.1192, N.1193, M.1197 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.137, N.171, V.198 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 6 residues within 4Å: Chain B: E.346, N.371, S.374, F.378, T.616, Q.619 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.378 NAG-NAG.8: 4 residues within 4Å: Chain B: D.727, N.738, T.740, A.741 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: V.1192, N.1193, M.1197 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain B: S.654, I.673, N.675 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain C: N.137, N.171 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 6 residues within 4Å: Chain C: E.346, N.371, S.374, F.378, T.616, Q.619 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.378 NAG-NAG.14: 2 residues within 4Å: Chain C: P.446, N.449 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain C: D.727, N.738, T.740, A.741 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain C: A.932, A.933, N.936, G.940 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain C: V.1192, N.1193, M.1197 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain C: I.149, K.204, R.205, N.206 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 2 residues within 4Å: Chain C: 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.5: 6 residues within 4Å: Chain A: R.147, I.149, L.162, K.204, R.205, N.206 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 6 residues within 4Å: Chain B: R.147, I.149, L.162, K.204, R.205, N.206 No protein-ligand interaction detected (PLIP)

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

NAG.20: 1 residues within 4Å: Chain A: N.212 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: A.448, N.449 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.713 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: S.785, N.787 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: A.932, A.933, N.936, G.940 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: I.673, N.675 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: H.693, N.695, Y.759, K.761 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: E.646, V.647, N.648 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: N.63, Q.288 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: M.122, N.212 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.713 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: S.785, N.787 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain B: A.932, A.933, N.936, G.940 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: H.693, N.695, Y.759 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: V.647, N.648 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain B: N.449 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: V.1222, N.1223 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: V.211, N.212 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.713 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.787 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: H.693, N.695, Y.759 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: E.646, V.647, N.648 Ligand excluded by PLIP

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

8Z9.29: 16 residues within 4Å: Chain A: V.415, D.416, N.421, L.422, G.423 Chain C: F.370, M.372, L.375, M.376, A.381, A.391, A.392, I.394, Y.395, I.402, L.603 11 PLIP interactions: 7 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:F.370, C:L.375, C:L.375, C:A.381, C:I.394, C:I.402, A:V.415, A:N.421 Hydrogen bonds: C:Y.395, A:L.422, A:G.423 8Z9.38: 15 residues within 4Å: Chain A: F.370, M.372, L.375, A.381, A.391, A.392, I.394, F.399, I.402, L.603, L.605 Chain B: V.415, N.421, L.422, G.423 13 PLIP interactions: 3 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:V.415, A:F.370, A:L.375, A:L.375, A:A.381, A:I.394, A:I.394, A:F.399, A:I.402, A:L.605 Hydrogen bonds: B:L.422, B:G.423, A:Y.395 8Z9.39: 15 residues within 4Å: Chain B: F.370, M.372, L.375, M.376, A.381, A.391, Y.395, I.402, L.441, L.603 Chain C: V.415, D.416, N.421, L.422, G.423 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:F.370, B:L.375, B:L.375, B:A.381, B:I.402, B:L.441, B:L.603, C:V.415, C:N.421 Hydrogen bonds: B: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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
J

B
A

C
B

D
H

E
L

Spike protein

Human polyclonal Fab model with polyalanine backbone - Heavy chain

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