MolNFT v1 · #155983 · protein

Phascolosoma esculenta

6LPD · Ferritin: “Phascolosoma esculenta”. X-ray diffraction, 2 ligands (FE2, FE), 15 pockets (best druggability 0.78). MolNFT v1 #155983 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6LPD
Type: protein
Length: 1,020 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ferritin
Ligands: FE2, FE
Pockets: 15 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 74% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Ferritin	protein	170	74% helix, 1% strand	—

Ligands and binding sites

FE2 · Fe (II) ion · metal · 13 copies · chains A, B, C, E, D, F
FE · Fe (III) ion · metal · chains F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	102	0.78	0.98	18	empty
2	103	0.78	0.98	18	empty
3	106	0.77	0.97	20	empty
4	178	0.59	0.82	31	empty
5	84	0.56	0.86	20	FE2

Interfaces

9 interfaces between chains.

E–F · 1418 Å² buried · 19 hydrogen bonds · protein-protein
B–D · 1412 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 1412 Å² buried · 21 hydrogen bonds · protein-protein
B–E · 771 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 767 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6LPD · Phascolosoma esculenta · the same entry in another collection · chain F against F, 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
Elsewhere: RCSB PDB 6LPD · PDBe 6LPD

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