Research workbench
Crystal structure of a haloacid dehalogenase-like hydrolase (KPN_04322) from klebsiella pneumoniae subsp. pneumoniae mgh 78578 at 2.39 a resolution
Analyse Crystal structure of a haloacid dehalogenase-like hydrolase (KPN_04322) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PGV
- Type
- protein
- Length
- 1,031 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Haloacid dehalogenase-like hydrolase
- UniProt
- A6TGK6
- Ligands
- CA
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Haloacid dehalogenase-like hydrolase | protein | 259 | 37% helix, 24% strand | A6TGK6 |
| B, D | Haloacid dehalogenase-like hydrolase | protein | 257 | 38% helix, 25% strand | A6TGK6 |
| C | Haloacid dehalogenase-like hydrolase | protein | 258 | 37% helix, 24% strand | A6TGK6 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, B, C, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains A, C, B, D
- GOL · Glycerol · additive · 4 copies · chains A, C, B, 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 | 855 | 0.81 | 0.84 | 95 | EPE, GOL, CA |
| 2 | 988 | 0.76 | 0.78 | 72 | EDO |
| 3 | 464 | 0.68 | 0.79 | 38 | EDO |
| 4 | 155 | 0.58 | 0.83 | 30 | empty |
| 5 | 229 | 0.50 | 0.76 | 36 | CA, EPE, GOL |
Interfaces
4 interfaces between chains.
- A–C · 784 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 648 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 416 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 135 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 modified (engineered).
Compared structures
- 3PGV · Crystal structure of a haloacid dehalogenase-like hydrolase (KPN_04322) from Klebsiella… · 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 A6TGK6
- Elsewhere: RCSB PDB 3PGV · PDBe 3PGV · UniProt A6TGK6
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