MolNFT v1 · #69950 · protein
Crystal structure of macrophage migration inhibitory factor (mif) with imidazopyrimidinylphenyl inhibitor at 1.86A resolution
3L5S: “Crystal structure of macrophage migration inhibitory factor (mif) with imidazopyrimidinylphenyl inhibitor at…”. X-ray diffraction, 2 ligands (88X, SO4), 5 pockets (best druggability 0.83). MolNFT v1 #69950 on GenesisL1: 3D…
- PDB
- 3L5S
- Type
- protein
- Length
- 348 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
- 88X, SO4
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 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, C | Macrophage migration inhibitory factor (EC 5.3.2.1, 5.3.3.12) | protein | 117 | 38% helix, 30% strand | P14174 |
Ligands and binding sites
- 88X · 5-ethyl-2-(phenylcarbonyl)imidazo[1,2-a]pyrimidin-7(1H)-one · ligand · chains A, C
- SO4 · Sulfate ion · ion · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 478 | 0.83 | 0.90 | 50 | empty |
| 2 | 79 | 0.49 | 0.83 | 17 | 88X |
| 3 | 57 | 0.48 | 0.84 | 13 | empty |
| 4 | 56 | 0.47 | 0.84 | 13 | empty |
| 5 | 128 | 0.38 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1205 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1189 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1160 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3L5S · Crystal structure of macrophage migration inhibitory factor (MIF) with… · 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 3L5S · PDBe 3L5S · UniProt P14174
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