Research workbench
Structural and functional insights into macrophage migration inhibitory factor from oncomelania hupensis, the intermediate host of schistosoma japonicum
Analyse Structural and functional insights into macrophage migration inhibitory factor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LKW
- Type
- protein
- Length
- 548 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Macrophage migration inhibitory factor
- UniProt
- A0A1U9W5E8
- Ligands
- CL
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Macrophage migration inhibitory factor | protein | 138 | 43% helix, 21% strand | A0A1U9W5E8 |
| B | Macrophage migration inhibitory factor | protein | 139 | 42% helix, 22% strand | A0A1U9W5E8 |
| D | Macrophage migration inhibitory factor | protein | 137 | 41% helix, 22% strand | A0A1U9W5E8 |
| C | Macrophage migration inhibitory factor | protein | 134 | 34% helix, 23% strand | A0A1U9W5E8 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.82 | 0.95 | 29 | CL |
| 2 | 629 | 0.71 | 0.79 | 42 | empty |
| 3 | 346 | 0.63 | 0.79 | 32 | empty |
| 4 | 132 | 0.63 | 0.86 | 24 | empty |
| 5 | 91 | 0.38 | 0.76 | 18 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1219 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1186 Ų buried · 23 hydrogen bonds · protein-protein
- D–C · 1145 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 430 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 112 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6LKW · Structural and functional insights into macrophage migration inhibitory factor from… · 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 A0A1U9W5E8
- Elsewhere: RCSB PDB 6LKW · PDBe 6LKW · UniProt A0A1U9W5E8
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