MolNFT v1 · #121151 · protein
Xylose isomerase-like tim BARREL/4-hydroxyphenylpyruvate dioxygenase fusion protein
5HMQ: “Xylose isomerase-like tim BARREL/4-hydroxyphenylpyruvate dioxygenase fusion protein”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.91). MolNFT v1 #121151 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5HMQ
- Type
- protein
- Length
- 3,732 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxyphenylpyruvate dioxygenase
- EC
- 4.2.1.118
- UniProt
- Q88JU3
- Ligands
- MG
- Pockets
- 20 · best druggability 0.91
Structure
x-ray diffraction · 6 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxyphenylpyruvate dioxygenase (EC 4.2.1.118) | protein | 621 | 38% helix, 24% strand | Q88JU3 |
| B | 4-hydroxyphenylpyruvate dioxygenase (EC 4.2.1.118) | protein | 621 | 38% helix, 23% strand | Q88JU3 |
| C | 4-hydroxyphenylpyruvate dioxygenase (EC 4.2.1.118) | protein | 622 | 38% helix, 25% strand | Q88JU3 |
| D | 4-hydroxyphenylpyruvate dioxygenase (EC 4.2.1.118) | protein | 624 | 38% helix, 23% strand | Q88JU3 |
| E | 4-hydroxyphenylpyruvate dioxygenase (EC 4.2.1.118) | protein | 621 | 38% helix, 24% strand | Q88JU3 |
| F | 4-hydroxyphenylpyruvate dioxygenase (EC 4.2.1.118) | protein | 623 | 38% helix, 24% strand | Q88JU3 |
Ligands and binding sites
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D, E, F
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 | 1091 | 0.91 | 0.94 | 163 | empty |
| 2 | 815 | 0.90 | 0.94 | 109 | empty |
| 3 | 766 | 0.88 | 0.92 | 107 | empty |
| 4 | 802 | 0.88 | 0.91 | 100 | empty |
| 5 | 282 | 0.83 | 0.94 | 47 | empty |
Interfaces
5 interfaces between chains.
- B–F · 3593 Ų buried · 34 hydrogen bonds · protein-protein
- D–E · 3570 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 3493 Ų buried · 33 hydrogen bonds · protein-protein
- A–F · 304 Ų buried · 3 hydrogen bonds · protein-protein
- D–F · 26 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 modified (engineered).
Compared structures
- 5HMQ · xylose isomerase-like TIM barrel/4-hydroxyphenylpyruvate dioxygenase fusion protein · the same entry in another collection · chain F against F, TM-score 1.00
- Q88JU3 · AlphaFold monomer V2.0 prediction for 3-dehydroshikimate dehydratase (Q88JU3) · a predicted model of the same protein · chain C against A, TM-score 0.94
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 Q88JU3
- Elsewhere: RCSB PDB 5HMQ · PDBe 5HMQ · UniProt Q88JU3
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