Research workbench
Triuret hydrolase (trta) from herbaspirillum sp. bh-1 C162S bound with triuret
Analyse Triuret hydrolase (trta) from herbaspirillum sp. bh-1 C162S bound with triuret in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XJE
- Type
- protein
- Length
- 878 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine hydrolase
- UniProt
- A0A2N6JFX7
- Ligands
- TIU
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cysteine hydrolase | protein | 219 | 39% helix, 24% strand | A0A2N6JFX7 |
| B, D | Cysteine hydrolase | protein | 220 | 39% helix, 24% strand | A0A2N6JFX7 |
Ligands and binding sites
- TIU · tricarbonodiimidic diamide · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.69 | 0.94 | 25 | empty |
| 2 | 62 | 0.66 | 0.94 | 24 | empty |
| 3 | 58 | 0.64 | 0.94 | 24 | empty |
| 4 | 193 | 0.54 | 0.79 | 42 | empty |
| 5 | 169 | 0.41 | 0.73 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1748 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 1736 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 433 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6XJE · Triuret Hydrolase (TrtA) from Herbaspirillum sp. BH-1 C162S bound with triuret · the same entry in another collection · chain C against C, 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 A0A2N6JFX7
- Elsewhere: RCSB PDB 6XJE · PDBe 6XJE · UniProt A0A2N6JFX7
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