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De novo design of polynuclear transition metal clusters in helix bundles-4DH1

Analyse De novo design of polynuclear transition metal clusters in helix bundles-4DH1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5WLL
Type
protein
Length
104 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Helical bundle 4DH1
Ligands
ACE, ZN, NH2

Structure

x-ray diffraction · 1 distinct chain · 92% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, B, C, DHelical bundle 4DH1protein2692% helix, 0% strand—

Ligands and binding sites

  • ACE · Acetyl group · ligand · 4 copies · chains A, B, D, C
  • ZN · Zinc ion · metal · 5 copies · chains A, B, C, D
  • NH2 · Amino group · ion · 4 copies · chains A, B, C, D
  • GOL · Glycerol · additive · 2 copies · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Interfaces

6 interfaces between chains.

  • C–D · 729 Ų buried · 6 hydrogen bonds · protein-protein
  • A–B · 722 Ų buried · 8 hydrogen bonds · protein-protein
  • B–D · 94 Ų buried · 3 hydrogen bonds · protein-protein
  • A–C · 87 Ų buried · 2 hydrogen bonds · protein-protein
  • A–D · 38 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

  • 5WLL · De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH1 · the same entry in another collection · chain A against A, TM-score 1.00

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