SMTL ID : 6ds9.1

Elongated version of a de novo designed three helix bundle structure (GRa3D)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.34 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 2 residues within 4Å: Chain A: E.5, R.9 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.5, A:E.5, H2O.2 ZN.2: 4 residues within 4Å: Chain A: R.23, A.26 Ligands: SCN.3, SCN.4 No protein-ligand interaction detected (PLIP)

2 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.3: 5 residues within 4Å: Chain A: R.23, A.26, L.27 Ligands: ZN.2, SCN.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.23 SCN.4: 3 residues within 4Å: Chain A: A.26 Ligands: ZN.2, SCN.3 No protein-ligand interaction detected (PLIP)

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

CL.5: 2 residues within 4Å: Chain A: A.19, R.23 Ligand excluded by PLIP

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

EDO.6: 3 residues within 4Å: Chain A: Q.8, R.9, A.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.8, A:Q.8 EDO.7: 5 residues within 4Å: Chain A: S.46, E.47, A.49, A.50 Ligands: EDO.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.46 EDO.8: 4 residues within 4Å: Chain A: A.49, A.50, S.53 Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.53 EDO.9: 3 residues within 4Å: Chain A: K.59, P.64, E.67 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.59, A:P.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koebke, K.J. et al., Clarifying the Copper Coordination Environment in a de Novo Designed Red Copper Protein. Inorg Chem (2018)

Release Date

2018-10-03

Peptides

de novo designed three helix bundle GRa3D: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

de novo designed three helix bundle GRa3D