SMTL ID : 7sb3.1

Structure of OC43 spike in complex with polyclonal Fab1 (Donor 269)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-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: 2 residues within 4Å: Chain A: N.137, N.171 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: N.344, E.346, N.371, S.374, T.616 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: D.727, N.738, T.740, A.741 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.741 NAG-NAG.5: 3 residues within 4Å: Chain B: N.137, N.171, D.195 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: N.342, N.371, S.374, Q.619 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: D.727, N.738, T.740 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain B: R.147, L.162, K.204, R.205, N.206 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: N.695, Y.759, K.761 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain C: N.344, E.346, N.371, S.374, Q.619 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain C: F.726, D.727, N.738, T.740, A.741 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain C: V.1192, N.1193, M.1197 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain C: R.147, L.162, K.204, R.205, N.206 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain C: S.654, I.673, N.675 No protein-ligand interaction detected (PLIP)

1 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.4: 4 residues within 4Å: Chain A: T.148, L.162, K.204, N.206 No protein-ligand interaction detected (PLIP)

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

NAG.15: 2 residues within 4Å: Chain A: D.210, N.212 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: P.446, N.449 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.713 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.787 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: A.932, N.936 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: V.1192, N.1193, M.1197 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: I.673, N.675 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: N.695, Y.759 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: E.646, V.647, N.648 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: L.159, V.211, N.212 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: A.448, N.449 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.713 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.787 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: A.932, A.933, N.936, G.940 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: V.1192, N.1193, M.1197 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: I.673, T.674, N.675 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain B: E.646, V.647, N.648 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: V.1222, N.1223 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: N.137, N.171, T.196 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.212 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: P.446, N.449 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.713 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain C: N.787 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.695, Y.759 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: E.646, V.647, N.648 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: A.932, N.936, G.940 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: V.1222, N.1223 Ligand excluded by PLIP

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

8Z9.24: 13 residues within 4Å: Chain A: I.345, M.372, L.375, I.379, A.391, Y.395, I.402, L.441, L.603, L.605 Chain B: N.421, L.422, G.423 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.345, A:L.375, A:I.379, A:I.402, A:L.441, A:L.603, A:L.605 Hydrogen bonds: B:L.422 8Z9.25: 12 residues within 4Å: Chain A: V.415, N.421, L.422 Chain C: F.370, M.372, M.376, I.379, A.381, A.391, I.394, L.441, L.603 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.370, C:I.379, C:A.381, C:I.394, C:I.394, C:L.441, C:L.603, A:V.415 Hydrogen bonds: A:L.422 8Z9.44: 13 residues within 4Å: Chain B: M.372, L.375, M.376, I.379, A.381, A.391, I.394, Y.395, L.441, L.603 Chain C: N.421, L.422, G.423 10 PLIP interactions: 3 interactions with chain C, 7 interactions with chain B Hydrophobic interactions: C:N.421, B:L.375, B:L.375, B:I.379, B:A.381, B:L.441, B:L.603 Hydrogen bonds: C:L.422, C:G.423, B: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
J

B
A

C
B

D
H

E
L

Spike protein

Human polyclonal Fab model with polyalanine backbone - Heavy chain

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