MolNFT v1 · #48148 · protein
Crystal structure of haloacid delahogenase-like family hydrolase (NP_639141.1) from xanthomonas campestris at 1.81 a resolution
2PKE: “Crystal structure of haloacid delahogenase-like family hydrolase (NP_639141.1) from xanthomonas campestris at…”. X-ray diffraction, 2 ligands (MG, CL), 3 pockets (best druggability 0.66). MolNFT v1 #48148 on GenesisL1: 3D structure…
- PDB
- 2PKE
- Type
- protein
- Length
- 461 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Haloacid delahogenase-like family hydrolase
- UniProt
- Q8P4B4
- Ligands
- MG, CL
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Haloacid delahogenase-like family hydrolase | protein | 233 | 52% helix, 13% strand | Q8P4B4 |
| B | Haloacid delahogenase-like family hydrolase | protein | 228 | 47% helix, 14% strand | Q8P4B4 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.66 | 0.77 | 51 | MG, CL |
| 2 | 358 | 0.63 | 0.79 | 33 | CL |
| 3 | 441 | 0.63 | 0.77 | 50 | empty |
Interfaces
1 interface between chains.
- A–B · 1386 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 2PKE · Crystal structure of haloacid delahogenase-like family hydrolase (NP_639141.1) from… · 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 Q8P4B4
- Elsewhere: RCSB PDB 2PKE · PDBe 2PKE · UniProt Q8P4B4
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