SMTL ID : 8chy.1

Crystal structure of an 8-repeat consensus TPR superhelix with Zinc.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

13 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: D.21, D.23, E.24 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.21, A:D.23, H2O.1 ZN.2: 2 residues within 4Å: Chain A: D.36, R.38 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.36 ZN.3: 3 residues within 4Å: Chain A: D.55, D.57, E.58 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.57, A:D.57, A:E.58, A:E.58, H2O.1 ZN.4: 2 residues within 4Å: Chain A: D.70 Ligands: ZN.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.70, A:D.70 ZN.5: 2 residues within 4Å: Chain A: E.75 Ligands: ZN.4 No protein-ligand interaction detected (PLIP) ZN.6: 3 residues within 4Å: Chain A: D.89, D.91, E.92 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.91, A:E.92 ZN.7: 4 residues within 4Å: Chain A: D.123, D.125 Ligands: ZN.8, ZN.12 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.123 ZN.8: 4 residues within 4Å: Chain A: D.125, E.126 Ligands: ZN.7, ZN.12 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.125, A:D.125, A:E.126 ZN.9: 3 residues within 4Å: Chain A: D.157, D.159, E.160 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.159, A:E.160 ZN.10: 1 residues within 4Å: Chain A: E.163 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.163, A:E.163 ZN.11: 3 residues within 4Å: Chain A: D.259, D.261, E.262 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.261, A:E.262, A:E.262 ZN.12: 4 residues within 4Å: Chain A: D.123, E.126 Ligands: ZN.7, ZN.8 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.123 ZN.13: 1 residues within 4Å: Chain A: Q.132 No protein-ligand interaction detected (PLIP)

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

ACT.14: 4 residues within 4Å: Chain A: Y.85, N.116, Y.119, Y.131 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.116, A:Y.119 Hydrogen bonds: A:N.116, A:N.147 ACT.15: 4 residues within 4Å: Chain A: N.82, Y.85, Y.97, N.113 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.85 Water bridges: A:K.86 Salt bridges: A:K.86 ACT.16: 3 residues within 4Å: Chain A: S.209, E.211, A.212 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.209, A:E.211 ACT.17: 2 residues within 4Å: Chain A: N.252, Y.255 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.256

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

MPD.18: 3 residues within 4Å: Chain A: Q.268, L.271, E.272 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.268 Hydrogen bonds: A:E.272

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

CL.19: 0 residues within 4Å: (No contacts) 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

2024-02-21

Peptides

Crystal structure of an 8-repeat consensus TPR superhelix with Zinc.: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Crystal structure of an 8-repeat consensus TPR superhelix with Zinc.

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