MolNFT v1 · #84217 · protein
Structure of homogentisate 1,2-dioxygenase in complex with reaction intermediates of homogentisate with oxygen.
3ZDS: “Structure of homogentisate 1,2-dioxygenase in complex with reaction intermediates of homogentisate with…”. X-ray diffraction, 7 ligands (OMD, HMQ, M8O), 20 pockets (best druggability 0.85). MolNFT v1 #84217 on GenesisL1: 3D…
- PDB
- 3ZDS
- Type
- protein
- Length
- 5,110 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, HMQ, M8O, HQ9, FE, OXY, PO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homogentisate 1,2-dioxygenase (EC 1.13.11.5) | protein | 425 | 9% helix, 38% strand | Q88E47 |
| B, C, D, E, F, H, I, J, K, L | Homogentisate 1,2-dioxygenase (EC 1.13.11.5) | protein | 426 | 8% helix, 37% strand | Q88E47 |
| G | Homogentisate 1,2-dioxygenase (EC 1.13.11.5) | protein | 425 | 8% helix, 39% strand | Q88E47 |
Ligands and binding sites
- OMD · 2-(3,6-dihydroxyphenyl)acetic acid · ligand · 8 copies · chains B, D, E, G, H, I, J, K
- HMQ · 2-[(6R)-6-(dioxidanyl)-6-oxidanyl-3-oxidanylidene-cyclohexa-1,4-dien-1-yl]ethanoic acid · ligand · 2 copies · chains F, L
- M8O · 4-Maleylacetoacetic acid · ligand · chains A
- HQ9 · 2-(6-oxidanyl-3-oxidanylidene-cyclohexa-1,4-dien-1-yl)ethanoic acid · ligand · chains C
- FE · Fe (III) ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- OXY · Oxygen molecule · ion · chains A, C
- PO4 · Phosphate ion · ion · chains E
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 | 921 | 0.85 | 0.87 | 109 | empty |
| 2 | 934 | 0.84 | 0.85 | 132 | empty |
| 3 | 714 | 0.83 | 0.87 | 74 | empty |
| 4 | 155 | 0.82 | 0.98 | 37 | OMD |
| 5 | 528 | 0.81 | 0.88 | 52 | empty |
Interfaces
23 interfaces between chains.
- A–B · 2466 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 2461 Ų buried · 39 hydrogen bonds · protein-protein
- H–K · 2459 Ų buried · 40 hydrogen bonds · protein-protein
- I–K · 2455 Ų buried · 37 hydrogen bonds · protein-protein
- H–I · 2433 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 3ZDS · Structure of homogentisate 1,2-dioxygenase in complex with reaction intermediates of… · 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 3ZDS · PDBe 3ZDS · UniProt Q88E47
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