MolNFT v1 · #78875 · protein
Phenethylisothiocyanate covalently bound to macrophage migration inhibitory factor (mif)
3SMB: “Phenethylisothiocyanate covalently bound to macrophage migration inhibitory factor (mif)”. X-ray diffraction, 3 ligands (LE2, NA, CL), 5 pockets (best druggability 0.83). MolNFT v1 #78875 on GenesisL1: 3D structure, binding sites…
- PDB
- 3SMB
- 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
- LE2, NA, CL
- Pockets
- 5 · best druggability 0.83
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
- LE2 · N-(2-phenylethyl)thioformamide · ligand · 3 copies · chains A, C, B
- NA · Sodium ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 9 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 | 432 | 0.83 | 0.90 | 50 | empty |
| 2 | 100 | 0.60 | 0.86 | 14 | LE2 |
| 3 | 85 | 0.58 | 0.87 | 14 | LE2 |
| 4 | 87 | 0.57 | 0.86 | 13 | LE2 |
| 5 | 175 | 0.44 | 0.74 | 18 | CL, NA |
Interfaces
3 interfaces between chains.
- A–B · 1162 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1155 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1146 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 3SMB · Phenethylisothiocyanate Covalently Bound to Macrophage Migration Inhibitory Factor (MIF) · 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 3SMB · PDBe 3SMB · UniProt P14174
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