Research workbench
Macrophage migration inhibitory factor bound to covalent inhibitor RDR03785
Analyse Macrophage migration inhibitory factor bound to covalent inhibitor RDR03785 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J7P
- Type
- protein
- Length
- 342 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
- 6H1, 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 (EC 5.3.2.1, 5.3.3.12) | protein | 114 | 39% helix, 31% strand | P14174 |
Ligands and binding sites
- 6H1 · 6-{[4-(trifluoromethyl)phenyl]methyl}-2H-1,3-benzodioxol-5-ol · ligand · 3 copies · chains A, C, B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C
- GOL · Glycerol · additive · 3 copies · chains B, C
- IPA · Isopropyl alcohol · additive · 2 copies · chains A
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 | 586 | 0.81 | 0.86 | 67 | empty |
| 2 | 87 | 0.57 | 0.86 | 17 | 6H1 |
| 3 | 86 | 0.57 | 0.86 | 16 | 6H1 |
| 4 | 87 | 0.53 | 0.84 | 16 | 6H1 |
Interfaces
3 interfaces between chains.
- A–B · 1170 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1125 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1116 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 5J7P · Macrophage Migration Inhibitory Factor bound to Covalent Inhibitor RDR03785 · 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 5J7P · PDBe 5J7P · UniProt P14174
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