MolNFT v1 · #52386 · protein

A dodecameric thioferritin in the bacterial domain, characterization of the bacterioferritin-related protein from bacteroides fragilis

2VZB · Putative bacterioferritin-related protein: “A dodecameric thioferritin in the bacterial domain, characterization of the bacterioferritin-related protein…”. X-ray diffraction, 3 ligands (BEN, FE, MG), 1 pocket (best druggability…

PDB: 2VZB
Type: protein
Length: 669 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative bacterioferritin-related protein
UniProt: Q5LAA6
Ligands: BEN, FE, MG
Pockets: 1 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 78% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative bacterioferritin-related protein	protein	168	78% helix, 1% strand	Q5LAA6
B, C, D	Putative bacterioferritin-related protein	protein	167	78% helix, 1% strand	Q5LAA6

Ligands and binding sites

BEN · Benzamidine · ligand · chains A
FE · Fe (III) ion · metal · 8 copies · chains A, B, C, D
MG · Magnesium 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

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	357	0.59	0.77	48	empty

Interfaces

5 interfaces between chains.

A–B · 1281 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 755 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 555 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 544 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 537 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

2VZB · A Dodecameric Thioferritin in the Bacterial Domain, Characterization of the… · 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 Q5LAA6
Elsewhere: RCSB PDB 2VZB · PDBe 2VZB · UniProt Q5LAA6

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