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Crystal structure of M. penetrans ferritin

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

PDB: 7DIE
Type: protein
Length: 984 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ferritin
EC: 1.16.3.2
UniProt: Q8EWB1
Ligands: FE
Pockets: 13 · best druggability 0.45

Structure

x-ray diffraction · 1 distinct chain · 77% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Ferritin (EC 1.16.3.2)	protein	164	77% helix, 0% strand	Q8EWB1

Ligands and binding sites

FE · Fe (III) ion · metal · 36 copies · chains A, B, D, E, C, F

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

Pockets

13 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	68	0.45	0.82	18	empty
2	67	0.44	0.82	17	empty
3	103	0.38	0.75	17	empty
4	100	0.38	0.75	20	empty
5	56	0.36	0.79	19	empty

Interfaces

8 interfaces between chains.

C–D · 1202 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 1202 Å² buried · 5 hydrogen bonds · protein-protein
E–F · 1148 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 757 Å² buried · 9 hydrogen bonds · protein-protein
D–F · 731 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

7DIE · Crystal structure of M. penetrans Ferritin · the same entry in another collection · chain A against A, TM-score 1.00

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Every structure of UniProt Q8EWB1
Elsewhere: RCSB PDB 7DIE · PDBe 7DIE · UniProt Q8EWB1

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