Research workbench
Human D-dopachrome tautomerase (D-dt)/ macrophage migration inhibitory factor 2 (MIF2) complexed with the selective inhibitor 4-cppc
Analyse Human D-dopachrome tautomerase (D-dt)/ macrophage migration inhibitory factor 2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C5F
- Type
- protein
- Length
- 347 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-dopachrome decarboxylase
- EC
- 4.1.1.84
- UniProt
- P30046
- Ligands
- 7L9
- Pockets
- 2 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | D-dopachrome decarboxylase (EC 4.1.1.84) | protein | 117 | 40% helix, 28% strand | P30046 |
| B | D-dopachrome decarboxylase (EC 4.1.1.84) | protein | 113 | 39% helix, 27% strand | P30046 |
Ligands and binding sites
- 7L9 · 4-(3-carboxyphenyl)pyridine-2,5-dicarboxylic acid · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.45 | 0.74 | 25 | 7L9 |
| 2 | 122 | 0.39 | 0.74 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–B · 203 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 184 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6C5F · Human D-Dopachrome tautomerase (D-DT)/ macrophage migration inhibitory factor 2 (MIF2)… · the same entry in another collection · chain A against A, TM-score 1.00
- P30046 · AlphaFold monomer V2.0 prediction for D-dopachrome decarboxylase (P30046) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P30046
- Elsewhere: RCSB PDB 6C5F · PDBe 6C5F · UniProt P30046
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