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Crystal structure of macrophage migration inhibitory factor (mif) with hydroxyquinoline inhibitor 638 at 1.93A 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
- 3JSF
- Type
- protein
- Length
- 350 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
- XV1, 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 | 115 | 38% helix, 30% 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
- XV1 · 7-(2-fluorobenzyl)quinolin-8-ol · ligand · 3 copies · chains A, C, B
- SO4 · Sulfate ion · ion · 2 copies · chains 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 | 487 | 0.84 | 0.90 | 51 | empty |
| 2 | 60 | 0.54 | 0.87 | 14 | XV1 |
| 3 | 65 | 0.53 | 0.86 | 13 | XV1 |
| 4 | 76 | 0.50 | 0.84 | 18 | XV1 |
| 5 | 127 | 0.38 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1205 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1170 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1150 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 3JSF · Crystal structure of macrophage migration inhibitory factor (mif) with hydroxyquinoline… · 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 3JSF · PDBe 3JSF · UniProt P14174
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