Research workbench
Crystal structure of plasmodium falciparum mif in complex with 3-[(2- methyl-6-phenylpyridin-4-YL)OXY]PHENOL
Analyse Crystal structure of plasmodium falciparum mif in complex with 3-[(2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P7M
- Type
- protein
- Length
- 297 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Macrophage migration inhibitory factor-like protein
- UniProt
- Q6Q3H7
- Ligands
- 2OE
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Macrophage migration inhibitory factor-like protein | protein | 104 | 39% helix, 30% strand | Q6Q3H7 |
| B | Macrophage migration inhibitory factor-like protein | protein | 100 | 36% helix, 29% strand | Q6Q3H7 |
| C | Macrophage migration inhibitory factor-like protein | protein | 93 | 35% helix, 29% strand | Q6Q3H7 |
Ligands and binding sites
- 2OE · 3-[(2-methyl-6-phenylpyridin-4-yl)oxy]phenol · ligand · chains A, 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 | 790 | 0.74 | 0.79 | 65 | 2OE |
| 2 | 115 | 0.59 | 0.85 | 25 | empty |
| 3 | 92 | 0.55 | 0.85 | 25 | empty |
| 4 | 200 | 0.50 | 0.76 | 31 | empty |
| 5 | 73 | 0.33 | 0.75 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1051 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 939 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 638 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4P7M · Crystal structure of Plasmodium falciparum MIF in complex with… · 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 Q6Q3H7
- Elsewhere: RCSB PDB 4P7M · PDBe 4P7M · UniProt Q6Q3H7
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