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Thermodynamic hyperstability in parametrically designed helical bundles

Analyse Thermodynamic hyperstability in parametrically designed helical bundles in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4UOT
Type: protein
Length: 165 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Designed helical bundle 5H2L
Ligands: ACE
Pockets: 3 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 91% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Designed helical bundle 5H2L	protein	33	91% helix, 0% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 5 copies · chains A, B, C, D, E

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	87	0.77	0.98	24	empty
2	53	0.70	0.98	15	empty
3	185	0.60	0.81	20	empty

Interfaces

9 interfaces between chains.

C–D · 951 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 946 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 943 Å² buried · 6 hydrogen bonds · protein-protein
D–E · 926 Å² buried · 12 hydrogen bonds · protein-protein
A–E · 917 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

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

Compared structures

4UOT · Thermodynamic hyperstability in parametrically designed helical bundles · 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 4UOT · PDBe 4UOT

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