MolNFT v1 · #58644 · protein
Macrophage migration inhibitory factor (mif) complexed with inhibitor, 4-ipp.
3B9S: “Macrophage migration inhibitory factor (mif) complexed with inhibitor, 4-ipp.”. X-ray diffraction, 2 ligands (RW1, SO4), 4 pockets (best druggability 0.81). MolNFT v1 #58644 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3B9S
- Type
- protein
- Length
- 342 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Macrophage migration inhibitory factor
- UniProt
- P14174
- Ligands
- RW1, SO4
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Macrophage migration inhibitory factor | protein | 114 | 39% helix, 31% strand | P14174 |
Ligands and binding sites
- RW1 · 4-phenylpyrimidine · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 728 | 0.81 | 0.85 | 72 | empty |
| 2 | 116 | 0.57 | 0.84 | 21 | RW1 |
| 3 | 92 | 0.56 | 0.85 | 15 | RW1 |
| 4 | 71 | 0.54 | 0.86 | 13 | RW1 |
Interfaces
3 interfaces between chains.
- B–C · 1135 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1131 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1121 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 3B9S · Macrophage Migration Inhibitory Factor (MIF) complexed with Inhibitor, 4-IPP. · 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 3B9S · PDBe 3B9S · UniProt P14174
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