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Prawn ferritin to coordinate with heavy metal ions

Analyse Prawn ferritin to coordinate with heavy metal ions in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7EK7
Type: protein
Length: 1,014 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ferritin
EC: 1.16.3.1
UniProt: T2B7E1
Ligands: HG
Pockets: 13 · best druggability 0.81

Structure

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

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

Ligands and binding sites

HG · Mercury (II) ion · metal · 4 copies · chains C, A, D, E

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

Pockets

13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1134	0.81	0.82	104	empty
2	107	0.79	0.98	17	empty
3	95	0.77	0.98	20	empty
4	74	0.73	0.97	14	empty
5	839	0.73	0.78	52	empty

Interfaces

9 interfaces between chains.

A–B · 1417 Å² buried · 31 hydrogen bonds · protein-protein
C–F · 1407 Å² buried · 26 hydrogen bonds · protein-protein
D–E · 1352 Å² buried · 22 hydrogen bonds · protein-protein
C–B · 739 Å² buried · 7 hydrogen bonds · protein-protein
F–B · 555 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

7EK7 · prawn ferritin to coordinate with heavy metal ions · the same entry in another collection · chain C against C, 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 7EK7 · PDBe 7EK7 · UniProt T2B7E1

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