SMTL ID : 7n3t.1 (1 other biounit)

TrkA ECD complex with designed miniprotein ligand

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

hetero-1-1-mer

Ligands

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.1: 6 residues within 4Å: Chain A: V.65, N.87, S.89, F.90, E.108, V.110 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.90

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

NAG.2: 2 residues within 4Å: Chain A: E.32, N.33 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.33 NAG.3: 5 residues within 4Å: Chain A: T.35, E.36, R.60, N.61, R.85 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.60 Hydrogen bonds: A:N.61 NAG.4: 4 residues within 4Å: Chain A: G.285, N.324, T.326, S.339 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.324 Water bridges: A:G.285, A:T.326 NAG.5: 7 residues within 4Å: Chain A: R.123, Q.126, E.130, A.150, H.151, M.152, N.154 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.126 NAG.6: 1 residues within 4Å: Chain A: N.219 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.219 NAG.10: 2 residues within 4Å: Chain A: N.304, E.305 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.305 Hydrogen bonds: A:N.304, A:E.305

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

EDO.7: 6 residues within 4Å: Chain A: S.278, R.280, L.328, A.330, Q.335 Ligands: EDO.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.280 EDO.8: 5 residues within 4Å: Chain A: T.258, A.259, W.265, A.342, A.343 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.259, A:A.343 EDO.9: 6 residues within 4Å: Chain A: E.297, F.298, L.299, C.311 Chain B: F.30, K.31 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:K.31 Hydrogen bonds: A:C.311, A:R.313 EDO.11: 5 residues within 4Å: Chain A: A.330, N.331, P.332, G.334 Ligands: SO4.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.334 EDO.12: 3 residues within 4Å: Chain A: S.278, A.330 Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.278

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

SO4.13: 3 residues within 4Å: Chain A: H.257, T.258 Chain B: R.78 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.258 Water bridges: A:H.257 Salt bridges: A:H.257, B:R.78 SO4.14: 4 residues within 4Å: Chain A: A.191, G.192, W.193, K.206 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.193, A:W.193 Salt bridges: A:K.206 SO4.15: 5 residues within 4Å: Chain A: R.123, R.127, C.157, G.158, V.159 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.159 Salt bridges: A:R.123, A:R.127 SO4.16: 6 residues within 4Å: Chain A: S.253, V.254, Q.255, S.270, D.272, V.307 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.253, A:S.270 SO4.17: 3 residues within 4Å: Chain A: G.334, Q.335 Ligands: EDO.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.335

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

2022-04-20

Peptides

High affinity nerve growth factor receptor: A
Designed TrkA-binding miniprotein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

High affinity nerve growth factor receptor

Designed TrkA-binding miniprotein

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