Research workbench

1.90A resolution structure of bfrb (wild-type, C2221 form) from pseudomonas aeruginosa

Analyse 1.90A resolution structure of bfrb (wild-type, C2221 form) from pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5D8O
Type: protein
Length: 1,872 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ferroxidase
EC: 1.16.3.1
UniProt: Q9HY79
Ligands: HEM, K
Pockets: 20 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 79% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L	Ferroxidase (EC 1.16.3.1)	protein	156	79% helix, 0% strand	Q9HY79

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 7 copies · chains A, B, E, D, F, K, C, I, H, J, L
K · Potassium ion · metal · 3 copies · chains A, E, J, K, B, C, G, L, D, F, I
PG4 · Tetraethylene glycol · additive · 25 copies · chains A, B, J, C, E, G, D, F, I, L, H, K

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	88	0.73	0.96	12	empty
2	224	0.72	0.87	32	HEM
3	78	0.72	0.96	13	empty
4	220	0.72	0.87	31	HEM
5	214	0.71	0.87	33	HEM

Interfaces

27 interfaces between chains.

H–J · 906 Å² buried · 12 hydrogen bonds · protein-protein
C–I · 904 Å² buried · 12 hydrogen bonds · protein-protein
F–K · 901 Å² buried · 12 hydrogen bonds · protein-protein
B–E · 900 Å² buried · 12 hydrogen bonds · protein-protein
G–I · 563 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5D8O · 1.90A resolution structure of BfrB (wild-type, C2221 form) from Pseudomonas aeruginosa · 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 Q9HY79
Elsewhere: RCSB PDB 5D8O · PDBe 5D8O · UniProt Q9HY79

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.