Research workbench
Resting state of homogentisate 1,2-dioxygenase
Analyse Resting state of 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
- 4AQ2
- Type
- protein
- Length
- 5,055 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
- FE
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 8 distinct chains · 9% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homogentisate 1,2-dioxygenase (EC 1.13.11.5) | protein | 425 | 9% helix, 39% strand | Q88E47 |
| B, K | Homogentisate 1,2-dioxygenase (EC 1.13.11.5) | protein | 426 | 8% helix, 38% strand | Q88E47 |
| C, J | Homogentisate 1,2-dioxygenase (EC 1.13.11.5) | protein | 420 | 9% helix, 39% strand | Q88E47 |
| D | Homogentisate 1,2-dioxygenase (EC 1.13.11.5) | protein | 421 | 9% helix, 38% strand | Q88E47 |
| E, F, G | Homogentisate 1,2-dioxygenase (EC 1.13.11.5) | protein | 419 | 9% helix, 40% strand | Q88E47 |
| H | Homogentisate 1,2-dioxygenase (EC 1.13.11.5) | protein | 421 | 9% helix, 39% strand | Q88E47 |
| I | Homogentisate 1,2-dioxygenase (EC 1.13.11.5) | protein | 420 | 10% helix, 39% strand | Q88E47 |
| L | Homogentisate 1,2-dioxygenase (EC 1.13.11.5) | protein | 419 | 10% helix, 40% strand | Q88E47 |
Ligands and binding sites
- 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 | 742 | 0.84 | 0.87 | 88 | empty |
| 2 | 809 | 0.83 | 0.86 | 89 | empty |
| 3 | 831 | 0.83 | 0.86 | 79 | empty |
| 4 | 846 | 0.83 | 0.85 | 90 | empty |
| 5 | 743 | 0.83 | 0.86 | 80 | empty |
Interfaces
26 interfaces between chains.
- B–C · 2387 Ų buried · 36 hydrogen bonds · protein-protein
- J–L · 2372 Ų buried · 37 hydrogen bonds · protein-protein
- H–I · 2371 Ų buried · 36 hydrogen bonds · protein-protein
- G–I · 2371 Ų buried · 39 hydrogen bonds · protein-protein
- E–F · 2363 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 4AQ2 · resting state of 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 4AQ2 · PDBe 4AQ2 · UniProt Q88E47
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