Research workbench
Macrophage Migration Inhibitory Factor covalently complexed with phenethylisothiocyanate
Analyse Macrophage Migration Inhibitory Factor covalently complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F2K
- Type
- protein
- Length
- 342 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.53
- Source
- Homo sapiens
- Molecule
- Macrophage migration inhibitory factor
- EC
- 5.3.2.1, 5.3.3.12
- UniProt
- P14174
- Ligands
- LE2, SO4
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · resolution 1.53 · 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
- LE2 · N-(2-phenylethyl)thioformamide · ligand · 3 copies · chains A, C, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C
- IPA · Isopropyl alcohol · additive · 4 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 428 | 0.83 | 0.91 | 51 | empty |
| 2 | 88 | 0.58 | 0.86 | 13 | LE2 |
| 3 | 106 | 0.56 | 0.84 | 14 | LE2 |
| 4 | 78 | 0.56 | 0.86 | 12 | LE2 |
| 5 | 155 | 0.43 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1175 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1162 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1149 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 4F2K · Macrophage migration inhibitory factor covalently complexed with phenethylisothiocyanate · the same entry in another collection · chain A against A, TM-score 1.00
- P14174 · AlphaFold monomer V2.0 prediction for macrophage migration inhibitory factor (P14174) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 4F2K · PDBe 4F2K · UniProt P14174
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