Research workbench
Crystal structure of human tdo in complex with TRP, northeast structural genomics consortium target HR6161
Analyse Crystal structure of human tdo in complex with TRP, northeast structural… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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