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Tetragonal crystal structure of native horse spleen ferritin

Analyse Tetragonal crystal structure of native horse spleen ferritin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1IES
Type: protein
Length: 1,044 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ferritin
UniProt: P02791
Ligands: CD
Pockets: 7 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 75% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Ferritin	protein	174	75% helix, 0% strand	P02791

Ligands and binding sites

CD · Cadmium ion · metal · 5 copies · chains A, B, C, D, E, F

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

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	167	0.78	0.94	22	empty
2	255	0.57	0.78	33	CD
3	249	0.55	0.77	33	CD
4	232	0.55	0.78	33	empty
5	201	0.53	0.78	29	empty

Interfaces

9 interfaces between chains.

B–E · 1489 Å² buried · 20 hydrogen bonds · protein-protein
B–F · 711 Å² buried · 11 hydrogen bonds · protein-protein
C–E · 703 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 699 Å² buried · 5 hydrogen bonds · protein-protein
D–E · 689 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

1IES · Tetragonal crystal structure of native horse spleen ferritin · the same entry in another collection · chain F against F, TM-score 1.00
P02791 · AlphaFold monomer V2.0 prediction for ferritin light chain (P02791) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P02791
Elsewhere: RCSB PDB 1IES · PDBe 1IES · UniProt P02791

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