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2.20A resolution structure of bfrb (L68A) from pseudomonas aeruginosa

Analyse 2.20A resolution structure of bfrb (L68A) from pseudomonas aeruginosa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5D8Q
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, MG, ARS
Pockets: 20 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 78% 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	78% helix, 0% strand	Q9HY79

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 7 copies · chains A, B, C, H, E, G, I, D, J, F, K, L
MG · Magnesium ion · metal · 12 copies · chains B, L, A, K, G, C, E, H, D, I, J, F
ARS · Arsenic · metal · 3 copies · chains A, D, G, K, B, H, L, C, E

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	84	0.74	0.96	13	empty
2	219	0.72	0.87	29	HEM
3	212	0.72	0.87	33	HEM
4	210	0.72	0.87	32	HEM
5	197	0.72	0.88	33	HEM

Interfaces

26 interfaces between chains.

D–J · 924 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 903 Å² buried · 12 hydrogen bonds · protein-protein
C–H · 898 Å² buried · 14 hydrogen bonds · protein-protein
E–G · 892 Å² buried · 12 hydrogen bonds · protein-protein
F–K · 881 Å² buried · 13 hydrogen bonds · protein-protein

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 5D8Q · PDBe 5D8Q · UniProt Q9HY79

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