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
- 6AZS
- Type
- protein
- Length
- 911 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative amidase
- UniProt
- Q1M7F4
- Ligands
- C5S, CL
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative amidase | protein | 230 | 37% helix, 21% strand | Q1M7F4 |
| B, D | Putative amidase | protein | 226 | 38% helix, 22% strand | Q1M7F4 |
| C | Putative amidase | protein | 229 | 38% helix, 21% strand | Q1M7F4 |
Ligands and binding sites
- C5S · N-formyl-D-aspartic acid · ligand · 2 copies · chains B, C, A, D
- CL · Chloride ion · ion · chains A
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, B, D, C
- PEG · Di(hydroxyethyl)ether · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.85 | 0.91 | 42 | GOL |
| 2 | 179 | 0.81 | 0.96 | 36 | C5S |
| 3 | 150 | 0.81 | 0.97 | 34 | C5S |
| 4 | 378 | 0.74 | 0.85 | 42 | BTB |
| 5 | 375 | 0.74 | 0.85 | 41 | BTB |
Interfaces
6 interfaces between chains.
- B–C · 2005 Ų buried · 40 hydrogen bonds · protein-protein
- A–D · 1988 Ų buried · 39 hydrogen bonds · protein-protein
- B–D · 765 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 759 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 298 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6AZS · 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 6AZS · PDBe 6AZS · UniProt Q1M7F4
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