SMTL ID : 9db5.1

A DARPin fused to the 1TEL crystallization chaperone via a proline-alanine linker

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

monomer

Ligands

13 x ACY: ACETIC ACID(Non-functional Binders)

ACY.1: 7 residues within 4Å: Chain A: L.85, E.86, R.89, D.110, Y.114, L.119 Ligands: ACY.8 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.85, A:D.110, A:L.119 Hydrogen bonds: A:D.110, A:D.110 Salt bridges: A:R.89 ACY.2: 2 residues within 4Å: Chain A: I.220, D.221 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.221 ACY.3: 5 residues within 4Å: Chain A: E.163, L.166, K.167, V.197, H.201 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.200, A:H.201 ACY.4: 4 residues within 4Å: Chain A: R.97, E.130, V.131, K.134 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.134 Salt bridges: A:R.97, A:K.134 ACY.5: 9 residues within 4Å: Chain A: D.79, G.81, K.82, L.85, D.105, A.108, T.109 Ligands: NA.19, CL.22 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.109, A:T.109 ACY.6: 11 residues within 4Å: Chain A: Q.12, P.13, I.14, L.50, L.76, P.77, K.83, E.95, I.98, L.99 Ligands: ACY.7 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.14 Hydrogen bonds: A:I.14 ACY.7: 6 residues within 4Å: Chain A: Q.12, I.14, Y.15, K.83, E.95 Ligands: ACY.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Q.12, A:I.14, A:Y.15 Hydrogen bonds: A:Y.15, A:Y.15 Salt bridges: A:K.83 ACY.8: 4 residues within 4Å: Chain A: E.86, R.89, A.90 Ligands: ACY.1 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.86 ACY.9: 7 residues within 4Å: Chain A: Y.114, H.118, L.119, S.122, D.143, I.147, A.152 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.114, A:H.118, A:I.147 Hydrogen bonds: A:D.143, A:D.143 ACY.10: 6 residues within 4Å: Chain A: G.91, D.93, H.125, L.126, E.127, I.128 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:H.125 Hydrogen bonds: A:L.126, A:E.127, A:I.128 Water bridges: A:G.124, A:H.125 Salt bridges: A:H.125 ACY.11: 5 residues within 4Å: Chain A: S.142, G.146, Y.175, D.176, N.177 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.142 Water bridges: A:Y.175 ACY.12: 5 residues within 4Å: Chain A: Y.175, D.204, N.206, A.207, Q.208 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.208 ACY.13: 1 residues within 4Å: Chain A: T.109 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.109

8 x NA: SODIUM ION(Non-functional Binders)

NA.14: 3 residues within 4Å: Chain A: W.24, W.27, I.75 No protein-ligand interaction detected (PLIP) NA.15: 4 residues within 4Å: Chain A: D.79, L.80, G.81 Ligands: CL.22 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.79, A:D.79, A:L.80, A:G.81 NA.16: 2 residues within 4Å: Chain A: S.17, D.19 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.17 Water bridges: A:D.20 NA.17: 2 residues within 4Å: Chain A: S.17, N.45 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.45 NA.18: 3 residues within 4Å: Chain A: N.40, T.41, R.60 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.40 NA.19: 4 residues within 4Å: Chain A: N.107, A.108, T.109 Ligands: ACY.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.105, A:T.109 NA.20: 3 residues within 4Å: Chain A: L.52, T.53, Y.69 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.52, A:Y.69 Water bridges: A:N.102 NA.21: 2 residues within 4Å: Chain A: G.124, H.158 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.158 Water bridges: A:T.156

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.22: 5 residues within 4Å: Chain A: G.81, A.104, D.105 Ligands: ACY.5, NA.15 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pedroza Romo, M.J. et al., Optimal TELSAM-Target Protein Linker Character is Target Protein Dependent. To Be Published

Release Date

2024-10-09

Peptides

Transcription factor ETV6,DARPin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Transcription factor ETV6,DARPin