MolNFT v1 · #134886 · protein
Crystal structure of human tdo in complex with TRP, northeast structural genomics consortium target HR6161
5TIA · Tryptophan 2,3-dioxygenase: “Crystal structure of human tdo in complex with TRP, northeast structural genomics consortium target HR6161”. X-ray diffraction, 2 ligands (TRP, HEM), 20 pockets (best druggability 0.86). MolNFT v1…
- PDB
- 5TIA
- Type
- protein
- Length
- 1,343 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
- TRP, HEM
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 337 | 69% helix, 0% strand | P48775 |
| B | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 334 | 71% helix, 0% strand | P48775 |
| C | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 323 | 69% helix, 0% strand | P48775 |
| D | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 349 | 68% helix, 0% strand | P48775 |
Ligands and binding sites
- TRP · Tryptophan · ligand · 8 copies · chains A, B, C, D
- HEM · Protoporphyrin IX containing Fe · 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 412 | 0.86 | 0.94 | 43 | HEM, TRP |
| 2 | 416 | 0.86 | 0.94 | 41 | HEM, TRP |
| 3 | 523 | 0.86 | 0.92 | 75 | empty |
| 4 | 383 | 0.86 | 0.94 | 43 | HEM, TRP |
| 5 | 448 | 0.86 | 0.93 | 52 | HEM, TRP |
Interfaces
6 interfaces between chains.
- C–D · 2947 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 2918 Ų buried · 41 hydrogen bonds · protein-protein
- B–D · 1937 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 1924 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 803 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5TIA · Crystal structure of human TDO in complex with Trp, Northeast Structural Genomics… · the same entry in another collection · chain D against D, TM-score 1.00
- P48775 · AlphaFold monomer V2.0 prediction for tryptophan 2,3-dioxygenase (P48775) · a predicted model of the same protein · chain C 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 5TIA · PDBe 5TIA · UniProt P48775
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