MolNFT v1 · #114323 · protein
Structural and biochemical characterization of a non-canonical biuret hydrolase (biuh) from the cyanuric acid catabolism pathway of rhizobium leguminasorum bv. viciae 3841
5BK6 · Putative amidase: “Structural and biochemical characterization of a non-canonical biuret hydrolase (biuh) from the cyanuric acid…”. X-ray diffraction, 9 pockets (best druggability 0.85). MolNFT v1 #114323 on GenesisL1: 3D structure…
- PDB
- 5BK6
- Type
- protein
- Length
- 912 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative amidase
- UniProt
- Q1M7F4
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Putative amidase | protein | 230 | 38% helix, 21% strand | Q1M7F4 |
| B, D | Putative amidase | protein | 226 | 38% helix, 22% strand | Q1M7F4 |
Ligands and binding sites
- 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 530 | 0.85 | 0.91 | 42 | GOL |
| 2 | 174 | 0.81 | 0.96 | 37 | empty |
| 3 | 107 | 0.74 | 0.95 | 24 | empty |
| 4 | 355 | 0.73 | 0.85 | 44 | BTB |
| 5 | 279 | 0.72 | 0.86 | 38 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1973 Ų buried · 36 hydrogen bonds · protein-protein
- A–D · 1918 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 767 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 759 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 289 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5BK6 · 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 5BK6 · PDBe 5BK6 · UniProt Q1M7F4
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