SMTL ID : 7rdh.1

Crystal structure of the de novo designed binding protein H3mb in complex with the 1968 influenza A virus hemagglutinin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

hetero-3-3-2-mer

Ligands

5 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: T.31, N.32 Chain G: K.54 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:K.54 NAG-NAG.2: 3 residues within 4Å: Chain A: S.39, N.279, V.291 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain B: A.147, E.150, S.151, N.154, T.156 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain C: S.39, N.279, V.291, N.292 Chain D: E.69 1 PLIP interactions: 1 interactions with chain C Water bridges: C:K.293 NAG-NAG.7: 3 residues within 4Å: Chain E: T.31, N.32 Chain H: N.51 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.4: 3 residues within 4Å: Chain C: N.32, A.33, T.34 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 4 residues within 4Å: Chain E: S.39, N.279, V.291, K.293 No protein-ligand interaction detected (PLIP)

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

NAG.8: 3 residues within 4Å: Chain A: N.159, T.161 Chain C: S.213 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.213, C:S.213 NAG.9: 3 residues within 4Å: Chain C: N.159, T.161 Chain E: S.213 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.213, E:S.213, E:S.213 NAG.10: 6 residues within 4Å: Chain C: Q.74, N.75, E.113, F.114, I.115, R.144 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.113, C:F.114 NAG.11: 5 residues within 4Å: Chain E: Q.74, N.75, F.114, I.115, R.144 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.144, E:R.144 NAG.12: 3 residues within 4Å: Chain A: S.213 Chain E: N.159, T.161 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.213, A:S.213

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, L. et al., Design of protein-binding proteins from the target structure alone. Nature (2022)

Release Date

2022-05-04

Peptides

Hemagglutinin HA1 chain: ACE
Hemagglutinin HA2 chain: BDF
De novo designed protein H3mb: GH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

G
G

H
H

Hemagglutinin HA1 chain

Hemagglutinin HA2 chain

De novo designed protein H3mb

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