SMTL ID : 8bu0.1

Crystal structure of an 8 repeat consensus TPR superhelix with calcium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

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

ACT.1: 4 residues within 4Å: Chain A: D.23, E.24, E.27 Ligands: ACT.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.23 Water bridges: A:D.23, A:E.27 ACT.2: 3 residues within 4Å: Chain A: E.75, S.107, E.109 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.107, A:S.107 ACT.3: 4 residues within 4Å: Chain A: N.82, Y.85, K.86, N.113 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.113 Water bridges: A:K.86 Salt bridges: A:K.86 ACT.4: 1 residues within 4Å: Chain A: Y.28 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.28 ACT.5: 2 residues within 4Å: Chain A: E.27 Ligands: ACT.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.27 ACT.6: 5 residues within 4Å: Chain A: Y.17, N.48, Y.51, K.52, N.79 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.51 Hydrogen bonds: A:N.48, A:Y.63 Water bridges: A:K.52, A:K.52 Salt bridges: A:K.52 ACT.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ACT.20: 3 residues within 4Å: Chain A: Q.30, W.43, L.46 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.43, A:L.46 ACT.21: 2 residues within 4Å: Chain A: Q.19 Ligands: CA.9 No protein-ligand interaction detected (PLIP)

6 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.7: 1 residues within 4Å: Ligands: CA.8 No protein-ligand interaction detected (PLIP) CA.8: 2 residues within 4Å: Ligands: CA.7, CA.9 No protein-ligand interaction detected (PLIP) CA.9: 3 residues within 4Å: Chain A: Q.19 Ligands: CA.8, ACT.21 No protein-ligand interaction detected (PLIP) CA.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.11: 2 residues within 4Å: Chain A: D.23, E.24 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.23, A:E.24, A:E.24, H2O.1, H2O.2 CA.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

MPD.13: 1 residues within 4Å: Chain A: E.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.7 MPD.14: 3 residues within 4Å: Chain A: N.11, N.14 Ligands: MPD.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.14 MPD.15: 7 residues within 4Å: Chain A: Y.10, N.14, Y.17, K.18, N.45 Ligands: MPD.14, CL.18 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:N.14, A:Y.17, A:Y.17, A:K.18 Hydrogen bonds: A:N.45, A:N.45 Water bridges: A:Y.10 MPD.16: 8 residues within 4Å: Chain A: A.40, E.41, Y.44, D.70, S.73, E.75, A.76 Ligands: CL.18 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.40, A:Y.44, A:A.76 Hydrogen bonds: A:D.70, A:S.73, A:E.75 MPD.17: 4 residues within 4Å: Chain A: Y.10, D.36, S.39, E.41 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.10 Hydrogen bonds: A:E.41

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

CL.18: 2 residues within 4Å: Ligands: MPD.15, MPD.16 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liutkus, M. et al., Diverse crystalline protein scaffolds through metal-dependent polymorphism. Protein Sci. (2024)

Release Date

2023-12-13

Peptides

Consensus tetratricopeptide repeat protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Consensus tetratricopeptide repeat protein

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