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Crystal structure of MIF bound to compound 13
Analyse Crystal structure of MIF bound to compound 13 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E4A
- Type
- protein
- Length
- 342 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.475
- Source
- Homo sapiens
- Molecule
- Macrophage migration inhibitory factor
- EC
- 5.3.2.1, 5.3.3.12
- UniProt
- P14174
- Ligands
- HWL, NA, CL
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · resolution 1.475 · 1 distinct chain · 39% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Macrophage migration inhibitory factor (EC 5.3.2.1, 5.3.3.12) | protein | 114 | 39% helix, 31% strand | P14174 |
Ligands and binding sites
- HWL · Flavoxate · ligand · 2 copies · chains A, B, C
- NA · Sodium ion · metal · chains B, C
- CL · Chloride ion · ion · 11 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 472 | 0.84 | 0.91 | 50 | empty |
| 2 | 50 | 0.51 | 0.87 | 12 | CL |
| 3 | 85 | 0.47 | 0.81 | 19 | CL, HWL |
| 4 | 152 | 0.43 | 0.74 | 18 | CL |
Interfaces
3 interfaces between chains.
- A–B · 1155 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1153 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1112 Ų buried · 20 hydrogen bonds · protein-protein
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 7E4A · PDBe 7E4A · UniProt P14174
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