MolNFT v1 · #155865 · protein
Structural and functional insights into macrophage migration inhibitory factor from oncomelania hupensis, the intermediate host of schistosoma japonicum
6LKW: “Structural and functional insights into macrophage migration inhibitory factor from oncomelania hupensis, the…”. X-ray diffraction, 1 ligand (CL), 6 pockets (best druggability 0.82). MolNFT v1 #155865 on GenesisL1: 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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