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Positively supercharged variant of the computationally designed cage protein O3-33

Analyse Positively supercharged variant of the computationally designed cage protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6FDB
Type: protein
Length: 1,472 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Propanediol utilization protein
UniProt: A0A0M0QF47
Pockets: 11 · best druggability 0.56

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Propanediol utilization protein	protein	184	40% helix, 32% strand	A0A0M0QF47

Pockets

11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	196	0.56	0.79	29	empty
2	220	0.55	0.78	28	empty
3	160	0.55	0.81	29	empty
4	196	0.54	0.78	26	empty
5	125	0.50	0.80	27	empty

Interfaces

12 interfaces between chains.

G–H · 911 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 876 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 875 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 810 Å² buried · 14 hydrogen bonds · protein-protein
D–H · 477 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

6FDB · Positively supercharged variant of the computationally designed cage protein O3-33 · 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
Every structure of UniProt A0A0M0QF47
Elsewhere: RCSB PDB 6FDB · PDBe 6FDB · UniProt A0A0M0QF47

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