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
- 6AZN
- Type
- protein
- Length
- 1,809 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative amidase
- UniProt
- Q1M7F4
- Ligands
- PO4
- Pockets
- 14 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, F, G | Putative amidase | protein | 226 | 39% helix, 22% strand | Q1M7F4 |
| B | Putative amidase | protein | 223 | 38% helix, 22% strand | Q1M7F4 |
| H | Putative amidase | protein | 229 | 39% helix, 21% strand | Q1M7F4 |
| I | Putative amidase | protein | 227 | 39% helix, 22% strand | Q1M7F4 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, F, G, H, I
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, D, I, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.86 | 0.94 | 45 | empty |
| 2 | 485 | 0.86 | 0.93 | 47 | empty |
| 3 | 1163 | 0.79 | 0.81 | 100 | empty |
| 4 | 236 | 0.70 | 0.86 | 48 | EDO, PO4 |
| 5 | 267 | 0.68 | 0.84 | 31 | EDO |
Interfaces
16 interfaces between chains.
- A–D · 2028 Ų buried · 41 hydrogen bonds · protein-protein
- F–I · 2025 Ų buried · 42 hydrogen bonds · protein-protein
- G–H · 1991 Ų buried · 40 hydrogen bonds · protein-protein
- B–C · 1987 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 782 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6AZN · Structural and biochemical characterization of a non-canonical biuret hydrolase (BiuH)… · the same entry in another collection · 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 Q1M7F4
- Elsewhere: RCSB PDB 6AZN · PDBe 6AZN · UniProt Q1M7F4
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