Research workbench
D-dopachrome tautomerase (D-DT)/MACROPHAGE migration inhibitory factor 2 (MIF2) complexed with inhibitor 4-ipp
Analyse D-dopachrome tautomerase (D-DT)/MACROPHAGE migration inhibitory factor 2 (MIF2)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KAN
- Type
- protein
- Length
- 351 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-dopachrome tautomerase
- UniProt
- Q53Y51
- Ligands
- RW1, CL
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | D-dopachrome tautomerase | protein | 117 | 40% helix, 28% strand | Q53Y51 |
Ligands and binding sites
- RW1 · 4-phenylpyrimidine · ligand · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.71 | 0.75 | 84 | RW1, CL |
| 2 | 70 | 0.32 | 0.75 | 12 | RW1 |
| 3 | 51 | 0.30 | 0.75 | 13 | RW1, CL |
Interfaces
3 interfaces between chains.
- B–C · 326 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 188 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 95 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 3KAN · D-dopachrome tautomerase (D-DT)/macrophage migration inhibitory factor 2 (MIF2) complexed… · the same entry in another collection · chain B against B, 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 Q53Y51
- Elsewhere: RCSB PDB 3KAN · PDBe 3KAN · UniProt Q53Y51
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