Research workbench
Substrate bound homogentisate 1,2-dioxygenase
Analyse Substrate bound homogentisate 1,2-dioxygenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AQ6
- Type
- protein
- Length
- 5,105 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homogentisate 1,2-dioxygenase
- EC
- 1.13.11.5
- UniProt
- Q88E47
- Ligands
- OMD, FE
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, F, G, H, J, L | Homogentisate 1,2-dioxygenase (EC 1.13.11.5) | protein | 425 | 9% helix, 39% strand | Q88E47 |
| D | Homogentisate 1,2-dioxygenase (EC 1.13.11.5) | protein | 427 | 8% helix, 38% strand | Q88E47 |
| E, I, K | Homogentisate 1,2-dioxygenase (EC 1.13.11.5) | protein | 426 | 9% helix, 38% strand | Q88E47 |
Ligands and binding sites
- OMD · 2-(3,6-dihydroxyphenyl)acetic acid · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- FE · Fe (III) ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains K
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 | 523 | 0.83 | 0.89 | 77 | empty |
| 2 | 709 | 0.83 | 0.87 | 78 | empty |
| 3 | 471 | 0.82 | 0.89 | 68 | empty |
| 4 | 148 | 0.82 | 0.98 | 40 | FE, OMD |
| 5 | 148 | 0.82 | 0.98 | 38 | OMD |
Interfaces
26 interfaces between chains.
- G–I · 2369 Ų buried · 40 hydrogen bonds · protein-protein
- H–I · 2360 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 2353 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 2343 Ų buried · 35 hydrogen bonds · protein-protein
- D–E · 2331 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 4AQ6 · substrate bound homogentisate 1,2-dioxygenase · the same entry in another collection · chain L against L, 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 Q88E47
- Elsewhere: RCSB PDB 4AQ6 · PDBe 4AQ6 · UniProt Q88E47
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