Research workbench
Structural and biochemical characterization of a non-canonical biuret hydrolase (biuh) from the cyanuric acid catabolism pathway of rhizobium leguminasorum bv. viciae 3841
Analyse Structural and biochemical characterization of a non-canonical biuret hydrolase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AZQ
- Type
- protein
- Length
- 1,806 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative amidase
- UniProt
- Q1M7F4
- Ligands
- C5J, CA
- Pockets
- 13 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, H, A, B, D, E | Putative amidase | protein | 226 | 39% helix, 22% strand | Q1M7F4 |
| C, F | Putative amidase | protein | 225 | 40% helix, 22% strand | Q1M7F4 |
Ligands and binding sites
- C5J · dicarbonimidic diamide · ligand · 7 copies · chains G, H, A, B, C, D, E, F
- CA · Calcium ion · metal · 5 copies · chains G, C, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.87 | 0.94 | 46 | empty |
| 2 | 468 | 0.86 | 0.93 | 44 | empty |
| 3 | 1019 | 0.80 | 0.81 | 103 | empty |
| 4 | 136 | 0.68 | 0.89 | 21 | CA |
| 5 | 193 | 0.66 | 0.86 | 32 | empty |
Interfaces
16 interfaces between chains.
- C–D · 2051 Ų buried · 39 hydrogen bonds · protein-protein
- G–H · 2044 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 2023 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 2006 Ų buried · 38 hydrogen bonds · protein-protein
- H–C · 805 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6AZQ · Structural and biochemical characterization of a non-canonical biuret hydrolase (BiuH)… · the same entry in another collection · chain G against G, 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 Q1M7F4
- Elsewhere: RCSB PDB 6AZQ · PDBe 6AZQ · UniProt Q1M7F4
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