SMTL ID : 5vli.1

Computationally designed inhibitor peptide HB1.6928.2.3 in complex with influenza hemagglutinin (A/PuertoRico/8/1934)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-3-3-3-mer

Ligands

3 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.276, N.287 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain D: N.276, N.287 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain G: N.276, N.287 No protein-ligand interaction detected (PLIP)

3 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 B: E.147, E.150, N.154, T.156, K.161 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.147 Hydrogen bonds: B:E.147, B:E.147 NAG-NAG-BMA.9: 5 residues within 4Å: Chain E: E.147, E.150, N.154, T.156, K.161 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:E.147 Hydrogen bonds: E:E.147, E:E.147 NAG-NAG-BMA.16: 5 residues within 4Å: Chain H: E.147, E.150, N.154, T.156, K.161 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:E.147 Hydrogen bonds: H:E.147, H:E.147

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

NAG.3: 1 residues within 4Å: Chain A: N.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.12 NAG.10: 1 residues within 4Å: Chain D: N.12 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.12 NAG.17: 1 residues within 4Å: Chain G: N.12 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.12

3 x PGF: 2,5,8,11-TETRAOXATRIDECANE(Non-covalent)

PGF.4: 6 residues within 4Å: Chain A: Q.52, L.53, K.55, E.67, P.70, L.71 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.70 PGF.11: 6 residues within 4Å: Chain D: Q.52, L.53, K.55, E.67, P.70, L.71 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:P.70 PGF.18: 6 residues within 4Å: Chain G: Q.52, L.53, K.55, E.67, P.70, L.71 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:P.70

9 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 6 residues within 4Å: Chain B: I.10, W.14, H.25, Y.34, N.135, C.137 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.34 Water bridges: B:G.12, B:N.135 PEG.6: 6 residues within 4Å: Chain B: K.39, S.40, N.43, A.44, F.110, N.114 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.39 PEG.7: 6 residues within 4Å: Chain B: Q.42 Chain C: C.1, I.2, Y.24, V.39, C.40 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:C.1, C:C.40 PEG.12: 6 residues within 4Å: Chain E: I.10, W.14, H.25, Y.34, N.135, C.137 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Y.34 Water bridges: E:G.12, E:N.135 PEG.13: 6 residues within 4Å: Chain E: K.39, S.40, N.43, A.44, F.110, N.114 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.39 PEG.14: 6 residues within 4Å: Chain E: Q.42 Chain F: C.1, I.2, Y.24, V.39, C.40 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:C.1, F:C.40 PEG.19: 6 residues within 4Å: Chain H: I.10, W.14, H.25, Y.34, N.135, C.137 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:Y.34 Water bridges: H:G.12, H:N.135 PEG.20: 6 residues within 4Å: Chain H: K.39, S.40, N.43, A.44, F.110, N.114 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:K.39 PEG.21: 6 residues within 4Å: Chain H: Q.42 Chain I: C.1, I.2, Y.24, V.39, C.40 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:C.1, I:C.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chevalier, A. et al., Massively parallel de novo protein design for targeted therapeutics. Nature (2017)

Release Date

2017-09-27

Peptides

Hemagglutinin: ADG
Hemagglutinin: BEH
Computationally designed peptide HB1.6928.2.3: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

G
A

B
B

E
B

H
B

C
C

F
C

I
C

Hemagglutinin

Hemagglutinin

Computationally designed peptide HB1.6928.2.3

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