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Crystal structure of encapsulated ferritin domain from pyrococcus furiosus PFC_05175

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

PDB: 5N5E
Type: protein
Length: 2,922 residues
Chains: 30
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: PFC_05175
UniProt: I6U7J4
Ligands: FE
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 79% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
e, A, B, C, E, I, J, M, Q, Z, b, c	PFC_05175	protein	98	79% helix, 0% strand	I6U7J4
D, F, G, H, K, L, N, O, P, R, T, U, V, W, X, Y, a, d	PFC_05175	protein	97	79% helix, 0% strand	I6U7J4

Ligands and binding sites

FE · Fe (III) ion · metal · 30 copies · chains e, K, A, Z, B, Y, C, H, D, J, E, W, F, N, G, I, L, V, M, O, P, R, Q, d, T, U, X, b, a, c

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1134	0.78	0.80	128	empty
2	826	0.70	0.76	66	empty
3	723	0.69	0.76	60	empty
4	264	0.69	0.84	58	empty
5	171	0.64	0.85	41	empty

Interfaces

88 interfaces between chains.

C–d · 1930 Å² buried · 27 hydrogen bonds · protein-protein
E–c · 1925 Å² buried · 31 hydrogen bonds · protein-protein
E–W · 1920 Å² buried · 30 hydrogen bonds · protein-protein
a–c · 1919 Å² buried · 29 hydrogen bonds · protein-protein
F–N · 1915 Å² buried · 29 hydrogen bonds · protein-protein

Analyse

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Every structure of UniProt I6U7J4
Elsewhere: RCSB PDB 5N5E · PDBe 5N5E · UniProt I6U7J4

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