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A substrate bound structure of L-dopa dioxygenase from streptomyces sclerotialus
Analyse A substrate bound structure of L-dopa dioxygenase from streptomyces sclerotialus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ON3
- Type
- protein
- Length
- 879 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-dopa extradiol dioxygenase
- Ligands
- DAH, FE2
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-dopa extradiol dioxygenase | protein | 147 | 23% helix, 35% strand | — |
| B, F | L-dopa extradiol dioxygenase | protein | 148 | 22% helix, 35% strand | — |
| C, E | L-dopa extradiol dioxygenase | protein | 145 | 24% helix, 35% strand | — |
| D | L-dopa extradiol dioxygenase | protein | 146 | 22% helix, 35% strand | — |
Ligands and binding sites
- DAH · 3,4-dihydroxyphenylalanine · ligand · 6 copies · chains A, B, C, D, E, F
- FE2 · Fe (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 5 copies · chains A, B, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 573 | 0.74 | 0.81 | 82 | TRS |
| 2 | 447 | 0.72 | 0.82 | 43 | FE2, DAH |
| 3 | 327 | 0.68 | 0.82 | 42 | DAH, FE2 |
| 4 | 319 | 0.67 | 0.82 | 52 | empty |
| 5 | 371 | 0.67 | 0.81 | 44 | DAH, FE2 |
Interfaces
7 interfaces between chains.
- A–B · 2636 Ų buried · 41 hydrogen bonds · protein-protein
- E–F · 2615 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 2610 Ų buried · 41 hydrogen bonds · protein-protein
- B–D · 558 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 347 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6ON3 · A substrate bound structure of L-DOPA dioxygenase from Streptomyces sclerotialus · the same entry in another collection · chain B against B, 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
- Elsewhere: RCSB PDB 6ON3 · PDBe 6ON3
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