SMTL ID : 9qhb.1

Crystal structure of 16-repeat CTPR protein with eliminated coordination sites

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

monomer

Ligands

7 x CA: CALCIUM ION(Non-covalent)

CA.1: 2 residues within 4Å: Chain A: D.23, Q.53 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.23 CA.2: 2 residues within 4Å: Chain A: D.57 Ligands: CA.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.57, H2O.2 CA.3: 3 residues within 4Å: Chain A: D.57 Ligands: CA.2, CA.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.57, A:D.57 CA.4: 1 residues within 4Å: Chain A: R.72 No protein-ligand interaction detected (PLIP) CA.5: 1 residues within 4Å: Chain A: D.227 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.227, H2O.1, H2O.1, H2O.1 CA.6: 2 residues within 4Å: Chain A: Q.87 Ligands: CA.3 No protein-ligand interaction detected (PLIP) CA.7: 1 residues within 4Å: Chain A: E.58 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.58

5 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.8: 6 residues within 4Å: Chain A: A.40, E.41, Y.44, D.70, S.73, E.75 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:E.41, A:Y.44, A:Y.44, A:Y.44, A:E.75 Hydrogen bonds: A:D.70 MPD.9: 5 residues within 4Å: Chain A: A.74, E.75, Y.78, D.104, S.107 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.74 Hydrogen bonds: A:D.104 MPD.10: 5 residues within 4Å: Chain A: A.176, Y.180, D.206, S.209, E.211 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.176, A:Y.180, A:Y.180, A:D.206, A:E.211 Hydrogen bonds: A:D.206 MPD.11: 3 residues within 4Å: Chain A: Y.214, S.243, E.245 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.214, A:Y.214 Hydrogen bonds: A:S.243, A:E.245 MPD.12: 6 residues within 4Å: Chain A: A.142, E.143, Y.146, D.172, S.175, E.177 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.142, A:E.143, A:Y.146, A:Y.146 Hydrogen bonds: A:E.177, A:E.177

9 x ACT: ACETATE ION(Non-functional Binders)

ACT.13: 4 residues within 4Å: Chain A: A.6, Y.10, S.39, E.41 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.6 ACT.14: 2 residues within 4Å: Chain A: N.48, Y.51 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.51 Hydrogen bonds: A:N.79 Salt bridges: A:K.52 ACT.15: 4 residues within 4Å: Chain A: Y.51, N.82, Y.85, K.86 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.82, A:Y.85, A:K.86 ACT.16: 1 residues within 4Å: Chain A: Q.30 No protein-ligand interaction detected (PLIP) ACT.17: 3 residues within 4Å: Chain A: Y.17, K.18, N.45 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.17 Hydrogen bonds: A:N.45 ACT.18: 2 residues within 4Å: Chain A: E.109, S.141 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.109 ACT.19: 2 residues within 4Å: Chain A: N.116, Y.119 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.119 Salt bridges: A:K.120 ACT.20: 3 residues within 4Å: Chain A: Q.166, L.169, W.179 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.169, A:W.179 Hydrogen bonds: A:Q.166 ACT.21: 3 residues within 4Å: Chain A: D.206, R.208, S.209 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.208 Water bridges: A:R.208, A:A.210

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liutkus, M. et al., Rational Crystal Contact Engineering for Programmable Self-Assembled Protein Architectures. Angew.Chem.Int.Ed.Engl. (2025)

Release Date

2025-10-22

Peptides

Engineered tetratricopeptide repeat protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Engineered tetratricopeptide repeat protein