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Crystal structure of tryptophan 2,3-dioxygenase from ralstonia metallidurans
Analyse Crystal structure of tryptophan 2,3-dioxygenase from ralstonia metallidurans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NOX
- Type
- protein
- Length
- 4,137 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan 2,3-dioxygenase
- EC
- 1.13.11.11
- UniProt
- Q1LK00
- Ligands
- HEM
- Pockets
- 20 · best druggability 0.91
Structure
x-ray diffraction · 11 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 | 261 | 70% helix, 0% strand | Q1LK00 |
| B | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 266 | 67% helix, 0% strand | Q1LK00 |
| C | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 255 | 69% helix, 0% strand | Q1LK00 |
| D, H, I, P | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 259 | 70% helix, 0% strand | Q1LK00 |
| E | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 256 | 70% helix, 0% strand | Q1LK00 |
| F | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 260 | 68% helix, 0% strand | Q1LK00 |
| G | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 259 | 71% helix, 0% strand | Q1LK00 |
| J, O | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 257 | 70% helix, 0% strand | Q1LK00 |
| K | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 255 | 70% helix, 0% strand | Q1LK00 |
| L, N | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 260 | 69% helix, 0% strand | Q1LK00 |
| M | Tryptophan 2,3-dioxygenase (EC 1.13.11.11) | protein | 255 | 70% helix, 0% strand | Q1LK00 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1064 | 0.91 | 0.93 | 114 | empty |
| 2 | 764 | 0.89 | 0.92 | 75 | empty |
| 3 | 843 | 0.89 | 0.92 | 84 | empty |
| 4 | 679 | 0.88 | 0.93 | 85 | empty |
| 5 | 361 | 0.86 | 0.94 | 46 | HEM |
Interfaces
40 interfaces between chains.
- A–B · 3616 Ų buried · 60 hydrogen bonds · protein-protein
- E–F · 3250 Ų buried · 56 hydrogen bonds · protein-protein
- I–J · 3125 Ų buried · 56 hydrogen bonds · protein-protein
- K–L · 3114 Ų buried · 53 hydrogen bonds · protein-protein
- O–P · 3112 Ų buried · 50 hydrogen bonds · protein-protein
Compared structures
- 2NOX · Crystal structure of tryptophan 2,3-dioxygenase from Ralstonia metallidurans · the same entry in another collection · chain K against K, 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 Q1LK00
- Elsewhere: RCSB PDB 2NOX · PDBe 2NOX · UniProt Q1LK00
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