Research workbench
High-resolution crystal structure of HMIF2 with tartrate at the active site
Analyse High-resolution crystal structure of HMIF2 with tartrate at the active site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MSE
- Type
- protein
- Length
- 351 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
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | D-dopachrome decarboxylase (EC 4.1.1.84) | protein | 117 | 40% helix, 26% strand | P30046 |
Ligands and binding sites
- TLA · L(+)-tartaric acid · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 521 | 0.59 | 0.74 | 47 | empty |
| 2 | 308 | 0.56 | 0.76 | 26 | TLA |
| 3 | 210 | 0.48 | 0.75 | 27 | empty |
| 4 | 72 | 0.32 | 0.74 | 14 | TLA |
Interfaces
3 interfaces between chains.
- B–C · 321 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 152 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 96 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7MSE · High-resolution crystal structure of hMIF2 with tartrate at the active site · 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 B 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 7MSE · PDBe 7MSE · UniProt P30046
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