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Cystal structure of locked-trimer of human mif
Analyse Cystal structure of locked-trimer of human mif in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GUM
- Type
- protein
- Length
- 993 residues
- Chains
- 9
- 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
- CL
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 8 distinct chains · 36% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Macrophage migration inhibitory factor (EC 5.3.2.1, 5.3.3.12) | protein | 114 | 39% helix, 27% strand | P14174 |
| C | Macrophage migration inhibitory factor (EC 5.3.2.1, 5.3.3.12) | protein | 112 | 36% helix, 28% strand | P14174 |
| D | Macrophage migration inhibitory factor (EC 5.3.2.1, 5.3.3.12) | protein | 110 | 37% helix, 28% strand | P14174 |
| E | Macrophage migration inhibitory factor (EC 5.3.2.1, 5.3.3.12) | protein | 111 | 36% helix, 29% strand | P14174 |
| F | Macrophage migration inhibitory factor (EC 5.3.2.1, 5.3.3.12) | protein | 108 | 38% helix, 28% strand | P14174 |
| G | Macrophage migration inhibitory factor (EC 5.3.2.1, 5.3.3.12) | protein | 110 | 31% helix, 29% strand | P14174 |
| H | Macrophage migration inhibitory factor (EC 5.3.2.1, 5.3.3.12) | protein | 101 | 37% helix, 30% strand | P14174 |
| I | Macrophage migration inhibitory factor (EC 5.3.2.1, 5.3.3.12) | protein | 113 | 35% helix, 27% strand | P14174 |
Ligands and binding sites
- CL · Chloride ion · ion · 8 copies · chains A, B, C, H, E, F, D, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 911 | 0.83 | 0.84 | 81 | empty |
| 2 | 1123 | 0.79 | 0.81 | 84 | empty |
| 3 | 1160 | 0.77 | 0.79 | 78 | empty |
| 4 | 404 | 0.75 | 0.84 | 39 | empty |
| 5 | 87 | 0.59 | 0.87 | 23 | empty |
Interfaces
18 interfaces between chains.
- B–C · 1131 Ų buried · 19 hydrogen bonds · protein-protein
- H–I · 1103 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1058 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1044 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1037 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 4GUM · Cystal structure of locked-trimer of human 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 4GUM · PDBe 4GUM · UniProt P14174
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