MolNFT v1 · #177492 · protein

Prawn ferritin to coordinate with heavy metal ions

7EK5: “Prawn ferritin to coordinate with heavy metal ions”. X-ray diffraction, 2 ligands (FE, CD), 5 pockets (best druggability 0.78). MolNFT v1 #177492 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7EK5
Type: protein
Length: 676 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ferritin
EC: 1.16.3.1
UniProt: T2B7E1
Ligands: FE, CD
Pockets: 5 · best druggability 0.78

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Ferritin (EC 1.16.3.1)	protein	169	73% helix, 1% strand	T2B7E1

Ligands and binding sites

FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
CD · Cadmium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	85	0.78	0.99	15	empty
2	259	0.57	0.78	33	empty
3	169	0.45	0.74	26	empty
4	87	0.39	0.77	14	empty
5	72	0.39	0.79	16	empty

Interfaces

5 interfaces between chains.

A–B · 1508 Å² buried · 30 hydrogen bonds · protein-protein
B–D · 734 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 732 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 729 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 561 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

7EK5 · prawn ferritin to coordinate with heavy metal ions · 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 T2B7E1
Elsewhere: RCSB PDB 7EK5 · PDBe 7EK5 · UniProt T2B7E1

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