Research workbench
Crystal structure of yhjk (haloacid dehalogenase-like hydrolase protein) from bacillus subtilis
Analyse Crystal structure of yhjk (haloacid dehalogenase-like hydrolase protein) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GYG
- Type
- protein
- Length
- 1,042 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ntd biosynthesis operon putative hydrolase ntdb
- UniProt
- O07565
- Ligands
- MG
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ntd biosynthesis operon putative hydrolase ntdb | protein | 285 | 44% helix, 20% strand | O07565 |
| B | Ntd biosynthesis operon putative hydrolase ntdb | protein | 230 | 44% helix, 17% strand | O07565 |
| C | Ntd biosynthesis operon putative hydrolase ntdb | protein | 277 | 43% helix, 19% strand | O07565 |
| D | Ntd biosynthesis operon putative hydrolase ntdb | protein | 250 | 44% helix, 20% strand | O07565 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 707 | 0.82 | 0.86 | 88 | empty |
| 2 | 127 | 0.73 | 0.93 | 23 | empty |
| 3 | 163 | 0.59 | 0.83 | 36 | empty |
| 4 | 156 | 0.48 | 0.77 | 29 | empty |
| 5 | 163 | 0.45 | 0.76 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1871 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 1727 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 387 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 361 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 276 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 modified (engineered).
Compared structures
- 3GYG · Crystal structure of yhjK (haloacid dehalogenase-like hydrolase protein) from Bacillus… · the same entry in another collection · chain D against D, TM-score 1.00
- O07565 · AlphaFold monomer V2.0 prediction for kanosamine-6-phosphate phosphatase (O07565) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 O07565
- Elsewhere: RCSB PDB 3GYG · PDBe 3GYG · UniProt O07565
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