Research workbench
1.55 a crystal structure of macrophage migration inhibitory factor bound to iso-66 and a related compound
Analyse 1.55 a crystal structure of macrophage migration inhibitory factor bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K9G
- 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
- 1Q2, 1Q1, CL, SO4
- Pockets
- 5 · best druggability 0.83
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
- 1Q2 · (4R,6Z)-6-(3-fluoro-4-hydroxyphenyl)-4-hydroxy-6-iminohexan-2-one · ligand · 3 copies · chains A, B, C
- 1Q1 · 1-[(5S)-3-(3-fluoro-4-hydroxyphenyl)-4,5-dihydro-1,2-oxazol-5-yl]propan-2-one · ligand · chains A, B
- CL · Chloride ion · ion · 6 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 444 | 0.83 | 0.90 | 49 | empty |
| 2 | 72 | 0.57 | 0.87 | 17 | 1Q2, 1Q1 |
| 3 | 68 | 0.55 | 0.87 | 13 | 1Q2 |
| 4 | 62 | 0.55 | 0.87 | 13 | 1Q2 |
| 5 | 196 | 0.47 | 0.75 | 19 | CL |
Interfaces
3 interfaces between chains.
- A–B · 1208 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1186 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1144 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4K9G · 1.55 A Crystal Structure of Macrophage Migration Inhibitory Factor bound to ISO-66 and a… · 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 4K9G · PDBe 4K9G · UniProt P14174
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