MolNFT v1 · #46528 · protein
Structure of ohcu decarboxylase in complex with allantoin
2O73: “Structure of ohcu decarboxylase in complex with allantoin”. X-ray diffraction, 1 ligand (2AL), 4 pockets (best druggability 0.70). MolNFT v1 #46528 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2O73
- Type
- protein
- Length
- 992 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ohcu decarboxylase
- UniProt
- A1L259
- Ligands
- 2AL
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ohcu decarboxylase | protein | 165 | 70% helix, 0% strand | A1L259 |
| B, D, E | Ohcu decarboxylase | protein | 164 | 70% helix, 0% strand | A1L259 |
| C | Ohcu decarboxylase | protein | 167 | 72% helix, 0% strand | A1L259 |
| F | Ohcu decarboxylase | protein | 168 | 70% helix, 0% strand | A1L259 |
Ligands and binding sites
- 2AL · 1-(2,5-dioxo-2,5-dihydro-1H-imidazol-4-yl)urea · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 669 | 0.70 | 0.78 | 76 | empty |
| 2 | 618 | 0.69 | 0.78 | 72 | empty |
| 3 | 465 | 0.66 | 0.78 | 61 | empty |
| 4 | 141 | 0.45 | 0.76 | 24 | empty |
Interfaces
5 interfaces between chains.
- E–F · 1197 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1193 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1192 Ų buried · 16 hydrogen bonds · protein-protein
- C–F · 405 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 256 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2O73 · Structure of OHCU decarboxylase in complex with allantoin · the same entry in another collection · chain F against F, TM-score 1.00
- A1L259 · AlphaFold monomer V2.0 prediction for 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline… · a predicted model of the same protein · chain B against A, 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 A1L259
- Elsewhere: RCSB PDB 2O73 · PDBe 2O73 · UniProt A1L259
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