MolNFT v1 · #53654 · protein

The X-ray structure of ferritin from pyrococcus furiosus loaded with AG(I)

2X17 · Putative ferritin homolog: “The X-ray structure of ferritin from pyrococcus furiosus loaded with AG(I)”. X-ray diffraction, 1 ligand (AG), 20 pockets (best druggability 0.84). MolNFT v1 #53654 on GenesisL1: 3D structure, binding…

PDB: 2X17
Type: protein
Length: 4,110 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative ferritin homolog
UniProt: Q8U2T8
Ligands: AG
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 75% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
0, 2, 3, 6, 9, G, K, R	Putative ferritin homolog	protein	171	75% helix, 1% strand	Q8U2T8
1, 4, 5, 7, 8, H, I, J, L, Q, Z	Putative ferritin homolog	protein	172	74% helix, 1% strand	Q8U2T8
M, N, O, P, Y	Putative ferritin homolog	protein	170	75% helix, 1% strand	Q8U2T8

Ligands and binding sites

AG · Silver ion · metal · 33 copies · chains 0, I, 1, J, 7, O, 6, 2, K, 3, 9, Q, L, Y, 4, M, P, R, Z, 5, N, 8, G, H

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	209	0.84	0.96	28	empty
2	213	0.84	0.96	28	empty
3	210	0.83	0.95	28	empty
4	288	0.82	0.92	48	empty
5	288	0.81	0.91	49	empty

Interfaces

63 interfaces between chains.

H–Z · 2210 Å² buried · 27 hydrogen bonds · protein-protein
8–Q · 2209 Å² buried · 24 hydrogen bonds · protein-protein
0–I · 2201 Å² buried · 27 hydrogen bonds · protein-protein
1–J · 2199 Å² buried · 25 hydrogen bonds · protein-protein
3–L · 2187 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

2X17 · The X-ray structure of Ferritin from Pyrococcus furiosus loaded with Ag(I) · the same entry in another collection · chain 0 against 0, 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 Q8U2T8
Elsewhere: RCSB PDB 2X17 · PDBe 2X17 · UniProt Q8U2T8

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