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Crystal structure of macrophage migration inhibitory factor (mif) with imidazopyridazinol inhibitor at 1.80A resolution

Analyse Crystal structure of macrophage migration inhibitory factor (mif) with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3L5P
Type: protein
Length: 349 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Macrophage migration inhibitory factor
EC: 5.3.2.1, 5.3.3.12
UniProt: P14174
Ligands: 428, SO4
Pockets: 5 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 38% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Macrophage migration inhibitory factor (EC 5.3.2.1, 5.3.3.12)	protein	114	39% helix, 31% strand	P14174
B	Macrophage migration inhibitory factor (EC 5.3.2.1, 5.3.3.12)	protein	117	38% helix, 30% strand	P14174
C	Macrophage migration inhibitory factor (EC 5.3.2.1, 5.3.3.12)	protein	118	37% helix, 30% strand	P14174

Ligands and binding sites

428 · 2-(1-methylethyl)imidazo[1,2-b]pyridazin-6-ol · ligand · chains A, C
SO4 · Sulfate ion · ion · 2 copies · chains B, C
GOL · Glycerol · additive · 3 copies · chains A, C, B

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

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	496	0.84	0.90	51	empty
2	56	0.55	0.88	12	GOL
3	65	0.53	0.86	13	GOL
4	92	0.51	0.83	18	428, GOL
5	144	0.39	0.73	18	empty

Interfaces

3 interfaces between chains.

B–C · 1203 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1187 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 1152 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

3L5P · Crystal structure of macrophage migration inhibitory factor (MIF) with imidazopyridazinol… · 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 P14174
Elsewhere: RCSB PDB 3L5P · PDBe 3L5P · UniProt P14174

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