MolNFT v1 · #53091 · protein
Crystal structure of macrophage migration inhibitory factor from plasmodium berghei
2WKB: “Crystal structure of macrophage migration inhibitory factor from plasmodium berghei”. X-ray diffraction, 7 pockets (best druggability 0.77). MolNFT v1 #53091 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2WKB
- Type
- protein
- Length
- 674 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Macrophage migration inhibitory factor
- UniProt
- Q4YQW0
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Macrophage migration inhibitory factor | protein | 106 | 39% helix, 29% strand | Q4YQW0 |
| B | Macrophage migration inhibitory factor | protein | 111 | 37% helix, 28% strand | Q4YQW0 |
| C, F | Macrophage migration inhibitory factor | protein | 115 | 36% helix, 28% strand | Q4YQW0 |
| D | Macrophage migration inhibitory factor | protein | 111 | 40% helix, 27% strand | Q4YQW0 |
| E | Macrophage migration inhibitory factor | protein | 116 | 35% helix, 26% strand | Q4YQW0 |
Ligands and binding sites
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 434 | 0.77 | 0.86 | 66 | empty |
| 2 | 95 | 0.69 | 0.93 | 24 | empty |
| 3 | 212 | 0.55 | 0.79 | 35 | empty |
| 4 | 337 | 0.54 | 0.74 | 34 | GOL |
| 5 | 193 | 0.50 | 0.76 | 26 | empty |
Interfaces
7 interfaces between chains.
- D–E · 1321 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 1289 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1266 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1248 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1228 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (artifact).
Compared structures
- 2WKB · Crystal Structure of Macrophage Migration Inhibitory Factor from Plasmodium berghei · 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 Q4YQW0
- Elsewhere: RCSB PDB 2WKB · PDBe 2WKB · UniProt Q4YQW0
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