MolNFT v1 · #62141 · protein

Crystal structure of ferritin soaked with iron from pseudo-nitzschia multiseries

3E6S: “Crystal structure of ferritin soaked with iron from pseudo-nitzschia multiseries”. X-ray diffraction, 2 ligands (FE, SO4), 12 pockets (best druggability 0.72). MolNFT v1 #62141 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 3E6S
Type: protein
Length: 951 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ferritin
EC: 1.16.3.1
UniProt: B6DMH6
Ligands: FE, SO4
Pockets: 12 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 80% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, F	Ferritin (EC 1.16.3.1)	protein	159	79% helix, 1% strand	B6DMH6
B, C, E	Ferritin (EC 1.16.3.1)	protein	158	80% helix, 0% strand	B6DMH6

Ligands and binding sites

FE · Fe (III) ion · metal · 27 copies · chains A, B, C, D, E, F
SO4 · Sulfate ion · ion · 2 copies · chains A, B, F, C, D, E

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

Pockets

12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	55	0.72	0.98	10	empty
2	182	0.71	0.88	27	empty
3	158	0.69	0.88	24	empty
4	182	0.55	0.79	17	empty
5	143	0.45	0.77	31	empty

Interfaces

9 interfaces between chains.

A–C · 970 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 519 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 515 Å² buried · 6 hydrogen bonds · protein-protein
A–F · 475 Å² buried · 2 hydrogen bonds · protein-protein
B–F · 469 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

3E6S · Crystal structure of ferritin soaked with iron 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 3E6S · PDBe 3E6S · UniProt B6DMH6

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