MolNFT v1 · #136229 · protein
Crystal structure of H62A mutant of human macrophage migration inhibitory factor
5UMJ: “Crystal structure of H62A mutant of human macrophage migration inhibitory factor”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.84). MolNFT v1 #136229 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5UMJ
- 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
- SO4
- Pockets
- 4 · best druggability 0.84
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
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
- IPA · Isopropyl alcohol · additive · 5 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.84 | 0.91 | 49 | empty |
| 2 | 63 | 0.50 | 0.85 | 13 | IPA |
| 3 | 63 | 0.47 | 0.83 | 12 | IPA |
| 4 | 134 | 0.39 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1147 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1136 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1127 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5UMJ · Crystal structure of H62A mutant of human macrophage migration inhibitory factor · 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 5UMJ · PDBe 5UMJ · UniProt P14174
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