Research workbench

E. COLI bacterioferritin in its as-isolated form

Analyse E. COLI bacterioferritin in its as-isolated form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2HTN
Type: protein
Length: 1,264 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bacterioferritin
EC: 1.16.3.1
UniProt: P0ABD3
Ligands: HEM, FE
Pockets: 20 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 77% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Bacterioferritin (EC 1.16.3.1)	protein	158	77% helix, 0% strand	P0ABD3

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D, E, F, G, H
FE · Fe (III) ion · metal · 16 copies · chains A, B, C, D, E, F, G, H

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

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	244	0.73	0.87	29	HEM
2	220	0.73	0.88	32	HEM
3	212	0.72	0.87	31	HEM
4	205	0.69	0.86	28	HEM
5	50	0.61	0.93	12	empty

Interfaces

13 interfaces between chains.

A–B · 982 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 976 Å² buried · 13 hydrogen bonds · protein-protein
G–H · 966 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 966 Å² buried · 14 hydrogen bonds · protein-protein
A–H · 600 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

2HTN · E. coli bacterioferritin in its as-isolated form · the same entry in another collection · chain H against H, TM-score 1.00
P0ABD3 · AlphaFold monomer V2.0 prediction for bacterioferritin (P0ABD3) · a predicted model of the same protein · chain G against A, TM-score 0.99

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 P0ABD3
Elsewhere: RCSB PDB 2HTN · PDBe 2HTN · UniProt P0ABD3

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