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FE(II) loaded tegillarca granosa ferritin

Analyse FE(II) loaded tegillarca granosa ferritin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6L56
Type: protein
Length: 4,056 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ferritin
EC: 1.16.3.1
UniProt: D3JCC5
Ligands: FE2, NA, FE
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 74% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	Ferritin (EC 1.16.3.1)	protein	169	74% helix, 1% strand	D3JCC5

Ligands and binding sites

FE2 · Fe (II) ion · metal · 48 copies · chains A, F, J, B, D, G, C, L, M, E, N, O, H, R, S, I, T, V, K, Q, X, P, U, W
NA · Sodium ion · metal · 36 copies · chains A, E, B, H, C, K, D, M, F, I, G, T, U, J, R, L, N, P, O, X, Q, W, S, V
FE · Fe (III) ion · metal · 24 copies · chains A, E, B, H, C, K, G, D, M, F, I, T, U, J, R, L, N, P, O, X, Q, W, S, V

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	77	0.76	0.98	14	empty
2	78	0.75	0.98	16	empty
3	74	0.75	0.98	14	empty
4	95	0.75	0.96	20	empty
5	227	0.71	0.86	23	empty

Interfaces

72 interfaces between chains.

U–V · 1580 Å² buried · 30 hydrogen bonds · protein-protein
K–L · 1570 Å² buried · 28 hydrogen bonds · protein-protein
O–P · 1563 Å² buried · 27 hydrogen bonds · protein-protein
E–F · 1548 Å² buried · 26 hydrogen bonds · protein-protein
W–X · 1547 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

6L56 · Fe(II) loaded Tegillarca granosa 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 D3JCC5
Elsewhere: RCSB PDB 6L56 · PDBe 6L56 · UniProt D3JCC5

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