MolNFT v1 · #69948 · protein
Crystal structure of macrophage migration inhibitory factor (mif) with imidazopyridazinol inhibitor at 1.80A resolution
3L5P: “Crystal structure of macrophage migration inhibitory factor (mif) with imidazopyridazinol inhibitor at 1.80A…”. X-ray diffraction, 2 ligands (428, SO4), 5 pockets (best druggability 0.84). MolNFT v1 #69948 on GenesisL1: 3D…
- 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.
| Volume (ų) | 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 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1187 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1152 Ų 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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