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1.85 a resolution structure of wt bfrb from pseudomonas aeruginosa in complex with a protein-protein interaction inhibitor (analog 13)

Analyse 1.85 a resolution structure of wt bfrb from pseudomonas aeruginosa in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NLK
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: KTG, HEM, FE2
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

KTG · 4-{[3-(4-hydroxyphenyl)propyl]amino}-1H-isoindole-1, 3(2H)-dione · ligand · 12 copies · chains A, B, E, C, I, D, F, K, G, H, J, L
HEM · Protoporphyrin IX containing Fe · ligand · 7 copies · chains A, C, I, D, B, E, F, K, H, J, L
FE2 · Fe (II) ion · metal · 3 copies · chains A, E, J, K, B, C, G, L, D, F, I
PG4 · Tetraethylene glycol · additive · 17 copies · chains A, B, C, F, E, D, K, G, H, I, J, L

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	224	0.73	0.88	35	HEM
2	215	0.72	0.88	33	HEM
3	209	0.72	0.88	34	HEM
4	76	0.72	0.96	12	empty
5	233	0.71	0.86	34	HEM

Interfaces

27 interfaces between chains.

F–K · 904 Å² buried · 12 hydrogen bonds · protein-protein
C–I · 902 Å² buried · 12 hydrogen bonds · protein-protein
H–J · 898 Å² buried · 12 hydrogen bonds · protein-protein
B–E · 894 Å² buried · 12 hydrogen bonds · protein-protein
D–H · 561 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

6NLK · 1.85 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 6NLK · PDBe 6NLK · UniProt Q9HY79

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