MolNFT v1 · #111810 · protein
Mif in complex with 4-[(4-oxo-2-thioxo-1,3-thiazolan-3-yl) METHYL]BENZONITRILE
4Z1T · Macrophage migration inhibitory factor: “Mif in complex with 4-[(4-oxo-2-thioxo-1,3-thiazolan-3-yl) METHYL]BENZONITRILE”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.82). MolNFT v1 #111810 on GenesisL1: 3D…
- PDB
- 4Z1T
- Type
- protein
- Length
- 341 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
- SO4
- Pockets
- 2 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Macrophage migration inhibitory factor (EC 5.3.2.1, 5.3.3.12) | protein | 114 | 39% helix, 31% strand | P14174 |
| B | Macrophage migration inhibitory factor (EC 5.3.2.1, 5.3.3.12) | protein | 113 | 39% helix, 31% strand | P14174 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C
- IPA · Isopropyl alcohol · additive · 2 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 586 | 0.82 | 0.87 | 63 | SO4 |
| 2 | 61 | 0.40 | 0.80 | 16 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1131 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1130 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1114 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (nonstandard).
Compared structures
- 4Z1T · MIF in complex with 4-[(4-oxo-2-thioxo-1,3-thiazolan-3-yl)methyl]benzonitrile · 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 4Z1T · PDBe 4Z1T · UniProt P14174
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