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Crystal structure of a de novo designed octameric helical-bundle protein

Analyse Crystal structure of a de novo designed octameric helical-bundle protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6O35
Type: protein
Length: 401 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: De novo designed WSHC8
Pockets: 9 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 94% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	De novo designed WSHC8	protein	101	94% helix, 0% strand	—
B	De novo designed WSHC8	protein	100	94% helix, 0% strand	—
D	De novo designed WSHC8	protein	99	94% helix, 0% strand	—

Pockets

9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	322	0.68	0.82	40	empty
2	124	0.64	0.87	24	empty
3	253	0.57	0.78	28	empty
4	120	0.57	0.84	23	empty
5	193	0.56	0.79	27	empty

Interfaces

3 interfaces between chains.

B–C · 1395 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 1382 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 1262 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6O35 · Crystal structure of a de novo designed octameric helical-bundle protein · 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 6O35 · PDBe 6O35

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