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… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KER
- Type
- protein
- Length
- 468 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-dopachrome decarboxylase
- EC
- 4.1.1.84
- UniProt
- O35215
- Ligands
- RW1, NA, CL
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | D-dopachrome decarboxylase (EC 4.1.1.84) | protein | 117 | 41% helix, 32% strand | O35215 |
Ligands and binding sites
- RW1 · 4-phenylpyrimidine · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, C, B, D
- CL · Chloride ion · ion · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 384 | 0.75 | 0.85 | 38 | empty |
| 2 | 82 | 0.46 | 0.81 | 22 | empty |
| 3 | 58 | 0.43 | 0.82 | 18 | RW1, CL |
| 4 | 62 | 0.40 | 0.80 | 14 | RW1, CL |
| 5 | 57 | 0.40 | 0.81 | 17 | RW1, CL |
Interfaces
5 interfaces between chains.
- B–C · 1222 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1221 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1220 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 265 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 156 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 3KER · D-Dopachrome tautomerase (D-DT)/ macrophage migration inhibitory factor 2 (MIF2)… · the same entry in another collection · chain D against D, TM-score 1.00
- O35215 · AlphaFold monomer V2.0 prediction for D-dopachrome decarboxylase (O35215) · 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 O35215
- Elsewhere: RCSB PDB 3KER · PDBe 3KER · UniProt O35215
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.