MolNFT v1 · #121518 · protein
Structure-function analysis of functionally diverse members of the cyclic amide hydrolase family of toblerone fold enzymes
5HXZ · Barbiturase: “Structure-function analysis of functionally diverse members of the cyclic amide hydrolase family of toblerone…”. X-ray diffraction, 3 ligands (MHA, NA, CL), 15 pockets (best druggability 0.89). MolNFT v1 #121518 on…
- PDB
- 5HXZ
- Type
- protein
- Length
- 1,467 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Barbiturase
- EC
- 3.5.2.1
- UniProt
- Q8RSQ2
- Ligands
- MHA, NA, CL
- Pockets
- 15 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Barbiturase (EC 3.5.2.1) | protein | 367 | 32% helix, 27% strand | Q8RSQ2 |
| B | Barbiturase (EC 3.5.2.1) | protein | 366 | 32% helix, 27% strand | Q8RSQ2 |
Ligands and binding sites
- MHA · (carbamoylmethyl-carboxymethyl-amino)-acetic acid · ligand · 2 copies · chains A, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.89 | 0.91 | 156 | MHA |
| 2 | 51 | 0.68 | 0.97 | 18 | empty |
| 3 | 53 | 0.67 | 0.96 | 16 | empty |
| 4 | 104 | 0.64 | 0.89 | 21 | empty |
| 5 | 100 | 0.62 | 0.89 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1824 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 1810 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 1140 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 893 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 408 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5HXZ · Structure-function analysis of functionally diverse members of the cyclic amide hydrolase… · the same entry in another collection · chain D against D, TM-score 1.00
- Q8RSQ2 · AlphaFold monomer V2.0 prediction for barbiturase (Q8RSQ2) · a predicted model of the same protein · chain A 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 Q8RSQ2
- Elsewhere: RCSB PDB 5HXZ · PDBe 5HXZ · UniProt Q8RSQ2
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