MolNFT v1 · #95561 · protein

Crystal structure of iron soaked (5 min) ferritin from pseudo- nitzschia multiseries

4ITT: “Crystal structure of iron soaked (5 min) ferritin from pseudo- nitzschia multiseries”. X-ray diffraction, 1 ligand (FE), 14 pockets (best druggability 0.69). MolNFT v1 #95561 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4ITT
Type: protein
Length: 1,263 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 0.69

Structure

x-ray diffraction · 4 distinct chains · 79% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ferritin	protein	159	79% helix, 1% strand	B6DMH6
D, C, E, H	Ferritin	protein	158	80% helix, 0% strand	B6DMH6
F	Ferritin	protein	157	79% helix, 1% strand	B6DMH6
G	Ferritin	protein	156	79% helix, 0% strand	B6DMH6

Ligands and binding sites

FE · Fe (III) ion · metal · 6 copies · chains D, B, C, E, 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	188	0.69	0.87	22	empty
2	88	0.68	0.93	22	empty
3	135	0.54	0.81	17	empty
4	84	0.42	0.79	12	empty
5	87	0.41	0.78	16	empty

Interfaces

15 interfaces between chains.

C–H · 1094 Å² buried · 5 hydrogen bonds · protein-protein
A–E · 1072 Å² buried · 7 hydrogen bonds · protein-protein
B–F · 1045 Å² buried · 5 hydrogen bonds · protein-protein
D–G · 511 Å² buried · 7 hydrogen bonds · protein-protein
A–H · 505 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (alkylation).

Compared structures

4ITT · Crystal structure of iron soaked (5 min) ferritin from Pseudo-nitzschia multiseries · the same entry in another collection · chain F against F, 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 4ITT · PDBe 4ITT · UniProt B6DMH6

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