MolNFT v1 · #111811 · protein
Mif in complex with 1-(4-methylphenyl)-3-phenylprop-2-yn-1-one
4Z1U · Macrophage migration inhibitory factor: “Mif in complex with 1-(4-methylphenyl)-3-phenylprop-2-yn-1-one”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.86). MolNFT v1 #111811 on GenesisL1: 3D structure, binding…
- PDB
- 4Z1U
- Type
- protein
- Length
- 684 residues
- Chains
- 6
- 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 0.86
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Macrophage migration inhibitory factor (EC 5.3.2.1, 5.3.3.12) | protein | 114 | 39% helix, 30% strand | P14174 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 15 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 8 copies · chains A, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 627 | 0.86 | 0.90 | 79 | empty |
| 2 | 383 | 0.85 | 0.94 | 36 | empty |
| 3 | 112 | 0.50 | 0.81 | 19 | SO4 |
| 4 | 149 | 0.41 | 0.73 | 18 | empty |
| 5 | 139 | 0.40 | 0.73 | 18 | empty |
Interfaces
11 interfaces between chains.
- D–E · 1150 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1150 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1147 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1147 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1134 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (nonstandard).
Compared structures
- 4Z1U · MIF in complex with 1-(4-methylphenyl)-3-phenylprop-2-yn-1-one · 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 4Z1U · PDBe 4Z1U · UniProt P14174
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