MolNFT v1 · #140017 · protein

Crystal structure of bacterioferritin

5XX9: “Crystal structure of bacterioferritin”. X-ray diffraction, 1 ligand (FE2), 8 pockets (best druggability 0.76). MolNFT v1 #140017 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5XX9
Type: protein
Length: 960 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bacterioferritin
EC: 1.16.3.1
UniProt: Q9S2N0
Ligands: FE2
Pockets: 8 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 76% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Bacterioferritin (EC 1.16.3.1)	protein	162	75% helix, 0% strand	Q9S2N0
B, D	Bacterioferritin (EC 1.16.3.1)	protein	157	78% helix, 0% strand	Q9S2N0
E, F	Bacterioferritin (EC 1.16.3.1)	protein	161	76% helix, 0% strand	Q9S2N0

Ligands and binding sites

FE2 · Fe (II) ion · metal · 12 copies · chains A, B, C, D, E, F

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

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	983	0.76	0.79	99	empty
2	182	0.72	0.88	25	FE2
3	172	0.71	0.88	27	FE2
4	130	0.42	0.76	25	empty
5	133	0.42	0.75	27	empty

Interfaces

8 interfaces between chains.

A–B · 1214 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 1201 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 710 Å² buried · 6 hydrogen bonds · protein-protein
C–F · 671 Å² buried · 9 hydrogen bonds · protein-protein
D–F · 498 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

5XX9 · Crystal structure of Bacterioferritin · the same entry in another collection · chain F against F, TM-score 1.00
Q9S2N0 · AlphaFold monomer V2.0 prediction for bacterioferritin (Q9S2N0) · a predicted model of the same protein · chain D 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 Q9S2N0
Elsewhere: RCSB PDB 5XX9 · PDBe 5XX9 · UniProt Q9S2N0

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