SMTL ID : 8qzn.1

DARPin-Armadillo fusion protein with a selected Tyrosin pocket binding to the fused target peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

15 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 4 residues within 4Å: Chain A: D.5, L.6, K.9, L.25 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.5, A:K.9 EDO.2: 6 residues within 4Å: Chain A: S.4, L.6, G.7, G.29, A.30, D.31 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.4, A:G.29, A:D.31 Water bridges: A:S.4, A:S.4, A:S.4 EDO.3: 5 residues within 4Å: Chain A: Q.286, A.343, K.344, Y.345 Ligands: EDO.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.344 Water bridges: A:Q.286 EDO.4: 5 residues within 4Å: Chain A: P.225, V.228, Q.229, A.263, G.264 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.229 EDO.5: 10 residues within 4Å: Chain A: G.3, S.4, D.5, G.7, K.8, L.11, T.34, A.35, D.36, E.37 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.4, A:K.8, A:A.35 EDO.6: 3 residues within 4Å: Chain A: S.274, S.275, P.276 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.274 EDO.7: 5 residues within 4Å: Chain A: T.38, F.40, D.69, E.70, R.71 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.69, A:E.70, A:R.71, A:R.71 Water bridges: A:E.70, A:E.70 EDO.18: 4 residues within 4Å: Chain A: Q.18, D.19, D.20, E.21 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.18, A:D.19, A:D.20 EDO.19: 5 residues within 4Å: Chain A: N.66, N.68, T.74, A.100, T.101 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.68, A:T.101, A:T.101 Water bridges: A:T.101 EDO.20: 5 residues within 4Å: Chain A: A.163, H.164, S.167, W.202, N.206 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.206 Water bridges: A:H.164, A:N.206 EDO.21: 4 residues within 4Å: Chain A: N.254, G.295, N.296, E.297 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.254, A:N.296 Water bridges: A:G.295, A:G.295, A:E.297 EDO.22: 5 residues within 4Å: Chain A: Q.216, I.219, E.255, Q.256, A.259 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.216 EDO.23: 3 residues within 4Å: Chain A: R.283, Y.345 Ligands: EDO.3 No protein-ligand interaction detected (PLIP) EDO.24: 6 residues within 4Å: Chain A: N.68, D.69, E.70, R.71, G.72, V.103 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.69, A:G.72 EDO.25: 5 residues within 4Å: Chain A: R.187, E.188, S.190, S.191, P.192 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.190 Water bridges: A:S.191

10 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 5 residues within 4Å: Chain A: G.50, H.51, L.52, G.53 Ligands: SO4.17 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.52, A:G.53 Water bridges: A:I.54 SO4.9: 4 residues within 4Å: Chain A: G.116, H.117, L.118, E.119 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.118, A:E.119 Water bridges: A:H.117, A:I.120 SO4.10: 5 residues within 4Å: Chain A: G.83, H.84, L.85, E.86 Ligands: SO4.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.85, A:E.86 Water bridges: A:H.84, A:H.84 SO4.11: 7 residues within 4Å: Chain A: G.50, L.52, H.84, L.85, E.86, I.87 Ligands: SO4.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.86, A:I.87 Water bridges: A:G.83 Salt bridges: A:H.84 SO4.12: 4 residues within 4Å: Chain A: G.149, N.150, E.151, D.152 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.151, A:D.152, A:D.152 Water bridges: A:N.150, A:N.150 SO4.13: 3 residues within 4Å: Chain A: H.132, R.134, T.140 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.140 Water bridges: A:R.134, A:R.134 Salt bridges: A:R.134 SO4.14: 6 residues within 4Å: Chain A: L.118, D.152, S.191, N.193, H.196 Ligands: SO4.15 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.152, A:N.193 Water bridges: A:S.191, A:H.196, A:H.196 Salt bridges: A:H.196 SO4.15: 5 residues within 4Å: Chain A: E.151, D.152, R.155, H.196 Ligands: SO4.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.151 SO4.16: 3 residues within 4Å: Chain A: G.211, N.212, E.213 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.212, A:N.212 Water bridges: A:E.213 SO4.17: 4 residues within 4Å: Chain A: L.52, G.53, E.56 Ligands: SO4.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.53, A:E.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stark, Y. et al., Modular binder technology by NGS-aided, high-resolution selection in yeast of designed armadillo modules. Proc.Natl.Acad.Sci.USA (2024)

Release Date

2024-07-03

Peptides

DARPin-Armadillo fusion protein with Tyrosin pocket and linked target peptide: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DARPin-Armadillo fusion protein with Tyrosin pocket and linked target peptide