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Crystal structure of iron soaked (4H) ferritin from pseudo-nitzschia multiseries

Analyse Crystal structure of iron soaked (4H) ferritin from pseudo-nitzschia multiseries in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ISP
Type: protein
Length: 1,268 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ferritin
UniProt: B6DMH6
Ligands: FE
Pockets: 14 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 80% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, B, C, E, H	Ferritin	protein	159	81% helix, 1% strand	B6DMH6
F	Ferritin	protein	158	80% helix, 1% strand	B6DMH6
G	Ferritin	protein	156	80% helix, 0% strand	B6DMH6

Ligands and binding sites

FE · Fe (III) ion · metal · 35 copies · chains A, D, B, C, E, F, G, H

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

Pockets

14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	51	0.73	0.99	10	empty
2	105	0.72	0.94	30	empty
3	202	0.71	0.87	25	empty
4	106	0.43	0.78	24	empty
5	135	0.42	0.76	29	empty

Interfaces

15 interfaces between chains.

C–H · 1042 Å² buried · 6 hydrogen bonds · protein-protein
A–E · 1022 Å² buried · 6 hydrogen bonds · protein-protein
B–F · 1011 Å² buried · 6 hydrogen bonds · protein-protein
A–H · 502 Å² buried · 9 hydrogen bonds · protein-protein
D–G · 501 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (alkylation).

Compared structures

4ISP · Crystal structure of iron soaked (4h) ferritin from Pseudo-nitzschia multiseries · 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 B6DMH6
Elsewhere: RCSB PDB 4ISP · PDBe 4ISP · UniProt B6DMH6

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