Research workbench

M. xanthus ferritin-like protein encc

Analyse M. xanthus ferritin-like protein encc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7S8T
Type: protein
Length: 800 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Encc
UniProt: A0A4Y6CD88
Ligands: FE
Pockets: 19 · best druggability 0.67

Structure

x-ray diffraction · 5 distinct chains · 71% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Encc	protein	82	70% helix, 0% strand	A0A4Y6CD88
B, C, D, F, G	Encc	protein	80	71% helix, 0% strand	A0A4Y6CD88
E, H	Encc	protein	78	74% helix, 0% strand	A0A4Y6CD88
I	Encc	protein	79	72% helix, 0% strand	A0A4Y6CD88
J	Encc	protein	83	66% helix, 0% strand	A0A4Y6CD88

Ligands and binding sites

FE · Fe (III) ion · metal · 7 copies · chains A, J, E, F, C, H, G, I

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

Pockets

19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	72	0.67	0.93	17	empty
2	52	0.65	0.95	18	empty
3	55	0.65	0.94	14	empty
4	77	0.62	0.90	18	empty
5	76	0.52	0.85	17	empty

Interfaces

20 interfaces between chains.

B–J · 1610 Å² buried · 22 hydrogen bonds · protein-protein
A–H · 1565 Å² buried · 14 hydrogen bonds · protein-protein
D–I · 1557 Å² buried · 18 hydrogen bonds · protein-protein
F–G · 1537 Å² buried · 11 hydrogen bonds · protein-protein
C–E · 1516 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

7S8T · M. xanthus ferritin-like protein EncC · 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 A0A4Y6CD88
Elsewhere: RCSB PDB 7S8T · PDBe 7S8T · UniProt A0A4Y6CD88

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