Research workbench
Crystal structure of macrophage migration inhibitory factor (mif) with glycerol at 1.70A resolution
Analyse Crystal structure of macrophage migration inhibitory factor (mif) with glycerol… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L5V
- 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
- SO4
- Pockets
- 5 · best druggability 0.83
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 | 117 | 38% helix, 30% strand | P14174 |
| B | Macrophage migration inhibitory factor (EC 5.3.2.1, 5.3.3.12) | protein | 114 | 39% helix, 31% 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
- SO4 · Sulfate ion · ion · 3 copies · chains A, C
- 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
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 488 | 0.83 | 0.90 | 51 | empty |
| 2 | 58 | 0.52 | 0.87 | 13 | GOL |
| 3 | 63 | 0.52 | 0.86 | 13 | GOL |
| 4 | 66 | 0.49 | 0.84 | 13 | GOL |
| 5 | 132 | 0.39 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1222 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1214 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1177 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3L5V · Crystal structure of macrophage migration inhibitory factor (MIF) with glycerol at 1.70A… · 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 3L5V · PDBe 3L5V · UniProt P14174
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