MolNFT v1 · #167132 · protein
Crystal structure of HTDO2 bound to inhibitor GNE1
6VBN · Tryptophan 2,3-dioxygenase: “Crystal structure of HTDO2 bound to inhibitor GNE1”. X-ray diffraction, 2 ligands (HEM, QVY), 20 pockets (best druggability 0.86). MolNFT v1 #167132 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6VBN
- Type
- protein
- Length
- 1,375 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan 2,3-dioxygenase
- EC
- 1.13.11.11
- UniProt
- P48775
- Ligands
- HEM, QVY
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 67% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 344 | 67% helix, 0% strand | P48775 |
| B, D | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 343 | 66% helix, 1% strand | P48775 |
| C | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 345 | 67% helix, 2% strand | P48775 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- QVY · 1,5-anhydro-2,3-dideoxy-3-[(5S)-5H-imidazo[5,1-a]isoindol-5-yl]-D-threo-pentitol · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.86 | 0.87 | 120 | empty |
| 2 | 905 | 0.86 | 0.87 | 102 | empty |
| 3 | 1061 | 0.85 | 0.86 | 81 | QVY, HEM |
| 4 | 1091 | 0.84 | 0.85 | 82 | HEM, QVY |
| 5 | 985 | 0.83 | 0.84 | 69 | HEM, QVY |
Interfaces
6 interfaces between chains.
- C–D · 2914 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 2903 Ų buried · 43 hydrogen bonds · protein-protein
- B–D · 1894 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1851 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 466 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6VBN · Crystal Structure of hTDO2 bound to inhibitor GNE1 · 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 P48775
- Elsewhere: RCSB PDB 6VBN · PDBe 6VBN · UniProt P48775
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