Research workbench
Crystal structure of human tryptophan 2,3-dioxygenase in complex with carbon monoxide and tryptophan
Analyse Crystal structure of human tryptophan 2,3-dioxygenase in complex with carbon… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UD5
- Type
- protein
- Length
- 1,394 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, CMO
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 4 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 351 | 71% helix, 0% strand | P48775 |
| B | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 347 | 69% helix, 0% strand | P48775 |
| C | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 343 | 70% helix, 0% strand | P48775 |
| D | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 353 | 70% 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
- CMO · Carbon monoxide · ion · 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 | 1040 | 0.90 | 0.92 | 149 | empty |
| 2 | 405 | 0.87 | 0.94 | 40 | HEM, CMO, TRP |
| 3 | 416 | 0.87 | 0.94 | 43 | HEM, CMO, TRP |
| 4 | 411 | 0.87 | 0.94 | 42 | HEM, CMO, TRP |
| 5 | 432 | 0.86 | 0.93 | 53 | HEM, CMO, TRP |
Interfaces
6 interfaces between chains.
- A–B · 2950 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 2940 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 1964 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1860 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 826 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6UD5 · Crystal structure of human tryptophan 2,3-dioxygenase in complex with carbon monoxide and… · 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 6UD5 · PDBe 6UD5 · UniProt P48775
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