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Crystal structure of the negatively supercharged variant FTN(NEG) of human heavy chain ferritin

Analyse Crystal structure of the negatively supercharged variant FTN(NEG) of human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5JKK
Type: protein
Length: 1,376 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ferritin heavy chain
EC: 1.16.3.1
UniProt: P02794
Ligands: MG, FE, CL
Pockets: 16 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain · 73% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Ferritin heavy chain (EC 1.16.3.1)	protein	172	73% helix, 0% strand	P02794

Ligands and binding sites

MG · Magnesium ion · metal · 17 copies · chains A, B, C, D, H, G, E, F
FE · Fe (III) ion · metal · 10 copies · chains A, C, F, G, B, D, E, H
CL · Chloride ion · ion · 2 copies · chains A, C, F, G, D, E

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	350	0.66	0.81	41	MG
2	74	0.50	0.84	14	empty
3	58	0.46	0.84	13	empty
4	97	0.46	0.80	16	empty
5	66	0.41	0.81	14	empty

Interfaces

15 interfaces between chains.

B–E · 1582 Å² buried · 34 hydrogen bonds · protein-protein
C–H · 1582 Å² buried · 32 hydrogen bonds · protein-protein
D–G · 1572 Å² buried · 33 hydrogen bonds · protein-protein
C–D · 695 Å² buried · 8 hydrogen bonds · protein-protein
F–H · 692 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5JKK · Crystal structure of the negatively supercharged variant Ftn(neg) of human heavy chain… · the same entry in another collection · chain H against H, TM-score 1.00
P02794 · AlphaFold monomer V2.0 prediction for ferritin heavy chain (P02794) · a predicted model of the same protein · chain F 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 P02794
Elsewhere: RCSB PDB 5JKK · PDBe 5JKK · UniProt P02794

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