MolNFT v1 · #169644 · protein
Triuret hydrolase (trta) from herbaspirillum sp. bh-1
6XIX · Cysteine hydrolase: “Triuret hydrolase (trta) from herbaspirillum sp. bh-1”. X-ray diffraction, 20 pockets (best druggability 0.79). MolNFT v1 #169644 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6XIX
- Type
- protein
- Length
- 1,758 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine hydrolase
- UniProt
- A0A2N6JFX7
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, G | Cysteine hydrolase | protein | 219 | 37% helix, 24% strand | A0A2N6JFX7 |
| C | Cysteine hydrolase | protein | 221 | 38% helix, 24% strand | A0A2N6JFX7 |
| D, E, F, H | Cysteine hydrolase | protein | 220 | 39% helix, 24% strand | A0A2N6JFX7 |
Ligands and binding sites
- BME · Beta-mercaptoethanol · additive · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 345 | 0.79 | 0.89 | 35 | BME |
| 2 | 363 | 0.79 | 0.88 | 39 | BME |
| 3 | 306 | 0.78 | 0.89 | 39 | BME |
| 4 | 291 | 0.78 | 0.90 | 36 | BME |
| 5 | 341 | 0.78 | 0.88 | 35 | BME |
Interfaces
8 interfaces between chains.
- C–D · 1698 Ų buried · 31 hydrogen bonds · protein-protein
- F–H · 1667 Ų buried · 26 hydrogen bonds · protein-protein
- A–G · 1654 Ų buried · 32 hydrogen bonds · protein-protein
- B–E · 1636 Ų buried · 30 hydrogen bonds · protein-protein
- B–G · 428 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (additive adduct).
Compared structures
- 6XIX · Triuret Hydrolase (TrtA) from Herbaspirillum sp. BH-1 · 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 A0A2N6JFX7
- Elsewhere: RCSB PDB 6XIX · PDBe 6XIX · UniProt A0A2N6JFX7
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