Research workbench
Macrophage migration inhibitory factor in complex with a naphthyridinone inhibitor (3A)
Analyse Macrophage migration inhibitory factor in complex with a naphthyridinone… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B1K
- Type
- protein
- Length
- 342 residues
- Chains
- 3
- 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
- C9G, SO4
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Macrophage migration inhibitory factor (EC 5.3.2.1, 5.3.3.12) | protein | 114 | 39% helix, 31% strand | P14174 |
Ligands and binding sites
- C9G · 2-[1-(4-hydroxyphenyl)-1H-1,2,3-triazol-4-yl]-7-methyl-1,7-naphthyridin-8(7H)-one · ligand · 3 copies · chains A, C, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C
- GOL · Glycerol · additive · chains A, B
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 | 418 | 0.84 | 0.92 | 47 | empty |
| 2 | 55 | 0.53 | 0.87 | 13 | C9G |
| 3 | 56 | 0.52 | 0.87 | 13 | C9G |
| 4 | 64 | 0.48 | 0.84 | 14 | C9G |
| 5 | 155 | 0.41 | 0.73 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1177 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1163 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1149 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6B1K · Macrophage Migration Inhibitory Factor in Complex with a Naphthyridi Inhibitor (3a) · 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 6B1K · PDBe 6B1K · UniProt P14174
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