MolNFT v1 · #121068 · protein

Crystal structure of the cftr inhibitory factor cif bound to a urea inhibitor

5HK9: “Crystal structure of the cftr inhibitory factor cif bound to a urea inhibitor”. X-ray diffraction, 1 ligand (64O), 10 pockets (best druggability 0.79). MolNFT v1 #121068 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5HK9
Type: protein
Length: 1,183 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cftr inhibitory factor
UniProt: A0A0M3KL26
Ligands: 64O
Pockets: 10 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 43% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cftr inhibitory factor	protein	296	42% helix, 20% strand	A0A0M3KL26
B, D	Cftr inhibitory factor	protein	297	43% helix, 20% strand	A0A0M3KL26
C	Cftr inhibitory factor	protein	293	43% helix, 20% strand	A0A0M3KL26

Ligands and binding sites

64O · N-(4-{[4'-(carbamoylamino)-6-hydroxybiphenyl-3-yl]oxy}-3,5-dichlorophenyl)propanamide · ligand · 3 copies · chains A, B, D

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

Pockets

10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	675	0.79	0.84	91	empty
2	286	0.78	0.90	49	empty
3	59	0.70	0.97	19	64O
4	156	0.63	0.85	25	64O
5	170	0.63	0.84	25	64O

Interfaces

5 interfaces between chains.

C–D · 1435 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1429 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 618 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 617 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 384 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 1 covalent (disulfide, covalent ligand).

Compared structures

5HK9 · Crystal structure of the CFTR inhibitory factor Cif bound to a urea inhibitor · 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 A0A0M3KL26
Elsewhere: RCSB PDB 5HK9 · PDBe 5HK9 · UniProt A0A0M3KL26

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