MolNFT v1 · #121519 · protein
Orotic acid hydrolase
5HY0 · Ring-opening amidohydrolase: “Orotic acid hydrolase”. X-ray diffraction, 11 pockets (best druggability 0.85). MolNFT v1 #121519 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5HY0
- Type
- protein
- Length
- 1,448 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ring-opening amidohydrolase
- EC
- 3.5.2.15
- UniProt
- E3JD18
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ring-opening amidohydrolase (EC 3.5.2.15) | protein | 362 | 31% helix, 26% strand | E3JD18 |
| B | Ring-opening amidohydrolase (EC 3.5.2.15) | protein | 359 | 30% helix, 26% strand | E3JD18 |
| C | Ring-opening amidohydrolase (EC 3.5.2.15) | protein | 364 | 31% helix, 26% strand | E3JD18 |
| D | Ring-opening amidohydrolase (EC 3.5.2.15) | protein | 363 | 31% helix, 26% strand | E3JD18 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 374 | 0.85 | 0.94 | 38 | empty |
| 2 | 383 | 0.84 | 0.93 | 39 | empty |
| 3 | 783 | 0.80 | 0.84 | 113 | empty |
| 4 | 1148 | 0.79 | 0.81 | 143 | empty |
| 5 | 287 | 0.72 | 0.85 | 30 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1482 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 1479 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 437 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 417 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 353 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
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 E3JD18
- Elsewhere: RCSB PDB 5HY0 · PDBe 5HY0 · UniProt E3JD18
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