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A de novo designed hexameric coiled coil cc-HEX2

Analyse A de novo designed hexameric coiled coil cc-HEX2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4PN9
Type: protein
Length: 177 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cc-HEX2
Ligands: ACE
Pockets: 1 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 90% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, F	Cc-HEX2	protein	29	93% helix, 0% strand	—
C, D, E	Cc-HEX2	protein	30	87% helix, 0% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 5 copies · chains A, B, C, D, F
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains E, F

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	513	0.85	0.90	48	empty

Interfaces

6 interfaces between chains.

A–F · 717 Å² buried · 2 hydrogen bonds · protein-protein
E–F · 708 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 706 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 703 Å² buried · 1 hydrogen bond · protein-protein
D–E · 702 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 covalent (covalent ligand).

Compared structures

4PN9 · A de novo designed hexameric coiled coil CC-Hex2 · 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 4PN9 · PDBe 4PN9

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