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Structure of a group I haloacid dehalogenase from pseudomonas putida strain PP3
Analyse Structure of a group I haloacid dehalogenase from pseudomonas putida strain PP3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BJX
- Type
- protein
- Length
- 1,211 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Halocarboxylic acid dehalogenase dehi
- EC
- 3.8.1.2
- UniProt
- Q8GJ84
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 60% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Halocarboxylic acid dehalogenase dehi (EC 3.8.1.2) | protein | 311 | 60% helix, 1% strand | Q8GJ84 |
| B, C | Halocarboxylic acid dehalogenase dehi (EC 3.8.1.2) | protein | 295 | 58% helix, 1% strand | Q8GJ84 |
| D | Halocarboxylic acid dehalogenase dehi (EC 3.8.1.2) | protein | 310 | 61% helix, 1% strand | Q8GJ84 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 16 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 932 | 0.82 | 0.84 | 111 | empty |
| 2 | 244 | 0.79 | 0.92 | 39 | empty |
| 3 | 267 | 0.64 | 0.81 | 29 | empty |
| 4 | 172 | 0.56 | 0.81 | 33 | empty |
| 5 | 168 | 0.54 | 0.80 | 28 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1800 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1747 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 405 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 86 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 69 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 modified (engineered).
Compared structures
- 3BJX · Structure of a Group I haloacid dehalogenase from Pseudomonas putida strain PP3 · 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 Q8GJ84
- Elsewhere: RCSB PDB 3BJX · PDBe 3BJX · UniProt Q8GJ84
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