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Crystal structure of haliangium ochraceum encapsulated ferritin

Analyse Crystal structure of haliangium ochraceum encapsulated ferritin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5N5F
Type: protein
Length: 916 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Encapsulated ferritin
UniProt: D0LZ73
Ligands: NA
Pockets: 14 · best druggability 0.61

Structure

x-ray diffraction · 2 distinct chains · 80% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F, H, I	Encapsulated ferritin	protein	91	80% helix, 0% strand	D0LZ73
B, C, D, E, G, J	Encapsulated ferritin	protein	92	80% helix, 0% strand	D0LZ73

Ligands and binding sites

NA · Sodium ion · metal · chains E

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

Pockets

14 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	287	0.61	0.79	49	empty
2	121	0.58	0.85	24	empty
3	88	0.55	0.85	18	empty
4	125	0.51	0.80	26	empty
5	100	0.41	0.77	17	empty

Interfaces

20 interfaces between chains.

C–D · 2468 Å² buried · 41 hydrogen bonds · protein-protein
B–J · 2450 Å² buried · 38 hydrogen bonds · protein-protein
E–G · 2409 Å² buried · 37 hydrogen bonds · protein-protein
A–I · 2396 Å² buried · 37 hydrogen bonds · protein-protein
F–H · 2387 Å² buried · 40 hydrogen bonds · protein-protein

Compared structures

5N5F · Crystal structure of Haliangium ochraceum encapsulated ferritin · 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 D0LZ73
Elsewhere: RCSB PDB 5N5F · PDBe 5N5F · UniProt D0LZ73

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