SMTL ID : 7n3t.2 (1 other biounit)

TrkA ECD complex with designed miniprotein ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

hetero-1-1-mer

Ligands

1 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: 7 residues within 4Å: Chain A: Y.38, 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

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

NAG.2: 7 residues within 4Å: Chain A: R.123, Q.126, E.130, A.150, H.151, M.152, N.154 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.126 Water bridges: A:A.150, A:N.154 NAG.3: 5 residues within 4Å: Chain A: L.282, G.285, N.324, T.326, S.339 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.324, A:T.326 Water bridges: A:G.285, A:G.285 NAG.4: 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.5: 2 residues within 4Å: Chain A: N.304, E.305 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.304, A:E.305, A:E.305 NAG.6: 1 residues within 4Å: Chain A: N.33 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.33 NAG.9: 2 residues within 4Å: Chain A: N.228, S.243 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.228, A:S.243 Water bridges: A:S.243, A:S.243 NAG.10: 1 residues within 4Å: Chain A: N.219 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.219 NAG.12: 4 residues within 4Å: Chain A: S.170, R.226, N.247, Q.274 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.226, A:N.247, A:Q.274

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

EDO.7: 4 residues within 4Å: Chain A: S.253, V.254, A.336, S.337 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.254, A:V.254, A:S.337 EDO.8: 7 residues within 4Å: Chain A: E.297, L.299, G.310, C.311 Chain B: F.30, K.31, V.34 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.297, A:E.297, A:R.313 EDO.11: 3 residues within 4Å: Chain A: F.295, T.296, E.297 No protein-ligand interaction detected (PLIP) EDO.13: 2 residues within 4Å: Chain A: G.334, Q.335 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.335, A:Q.335 Water bridges: A:G.334

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

SO4.14: 3 residues within 4Å: Chain A: H.257, T.258 Chain B: R.78 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.258, A:T.258, A:T.258 Water bridges: A:H.257 Salt bridges: A:H.257, B:R.78 SO4.15: 4 residues within 4Å: Chain A: A.191, G.192, W.193, K.206 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.193 Salt bridges: A:K.206 SO4.16: 4 residues within 4Å: Chain A: R.123, C.157, G.158, V.159 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.157, A:V.159 Salt bridges: A:R.123 SO4.17: 1 residues within 4Å: Chain A: R.186 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.186 SO4.18: 7 residues within 4Å: Chain A: S.253, V.254, Q.255, S.270, V.271, D.272, V.307 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.253, A:Q.255, A:D.272 Water bridges: A:D.272

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
B

B
D

High affinity nerve growth factor receptor

Designed TrkA-binding miniprotein

Related Entries With Identical Sequence