MolNFT v1 · #179430 · protein

1.90 a resolution structure of wt bfrb from pseudomonas aeruginosa in complex with a protein-protein interaction inhibitor km-5-50

7K5F · Ferroxidase: “1.90 a resolution structure of wt bfrb from pseudomonas aeruginosa in complex with a protein-protein…”. X-ray diffraction, 3 ligands (HEM, VXP, K), 20 pockets (best druggability 0.73). MolNFT v1 #179430 on GenesisL1…

PDB: 7K5F
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, VXP, K
Pockets: 20 · best druggability 0.73

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, E, C, I, D, F, K, H, J, L
VXP · 4-{[(3-chloro-5-hydroxyphenyl)methyl]amino}-1H-isoindole-1,3(2H)-dione · ligand · 6 copies · chains D, B, E, H, J, F, K, L
K · Potassium ion · metal · 3 copies · chains A, E, J, K, B, C, G, L, D, F, I

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	202	0.73	0.89	31	HEM
2	84	0.73	0.96	12	empty
3	203	0.72	0.88	33	HEM
4	210	0.71	0.87	33	HEM
5	74	0.71	0.96	12	empty

Interfaces

27 interfaces between chains.

B–E · 907 Å² buried · 12 hydrogen bonds · protein-protein
C–I · 906 Å² buried · 12 hydrogen bonds · protein-protein
H–J · 900 Å² buried · 12 hydrogen bonds · protein-protein
F–K · 900 Å² buried · 12 hydrogen bonds · protein-protein
D–K · 564 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

7K5F · 1.90 A resolution structure of WT BfrB from Pseudomonas aeruginosa in complex with a… · 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 7K5F · PDBe 7K5F · UniProt Q9HY79

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