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De novo design of polynuclear transition metal clusters in helix bundles-4EH2

Analyse De novo design of polynuclear transition metal clusters in helix bundles-4EH2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5WLK
Type: protein
Length: 104 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Helical bundle 4EH2
Ligands: ACE, ZN, NH2

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Helical bundle 4EH2	protein	26	92% helix, 0% strand	—

Ligands and binding sites

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

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

Interfaces

6 interfaces between chains.

C–D · 790 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 745 Å² buried · 12 hydrogen bonds · protein-protein
B–D · 98 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 92 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 48 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

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

Compared structures

5WLK · De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4EH2 · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 5WLK · PDBe 5WLK

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