MolNFT v1 · #139398 · protein
Crystal structure of macrophage migration inhibitory factor bound to mtx
5XEJ: “Crystal structure of macrophage migration inhibitory factor bound to mtx”. X-ray diffraction, 2 ligands (6UV, SO4), 5 pockets (best druggability 0.81). MolNFT v1 #139398 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5XEJ
- 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
- 6UV, SO4
- Pockets
- 5 · 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
- 6UV · (2~{R})-2-[[4-[[2,4-bis(azanyl)pteridin-6-yl]methyl-methyl-amino]phenyl]carbonylamino]pentanedioic acid · ligand · chains A, C
- SO4 · Sulfate ion · ion · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.81 | 0.89 | 51 | SO4 |
| 2 | 56 | 0.54 | 0.88 | 12 | 6UV |
| 3 | 57 | 0.50 | 0.86 | 13 | empty |
| 4 | 61 | 0.48 | 0.84 | 13 | empty |
| 5 | 114 | 0.36 | 0.73 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1186 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1167 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1152 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5XEJ · Crystal Structure of Macrophage Migration Inhibitory Factor bound to MTX · 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 B 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 5XEJ · PDBe 5XEJ · UniProt P14174
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