Research workbench
Crystal structure of a putative hydrolase from burkholderia cenocepacia
Analyse Crystal structure of a putative hydrolase from burkholderia cenocepacia in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QKU
- Type
- protein
- Length
- 1,695 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrolase
- UniProt
- B4ECX4
- Ligands
- NA, SO4
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydrolase | protein | 421 | 25% helix, 28% strand | B4ECX4 |
| B | Hydrolase | protein | 427 | 25% helix, 28% strand | B4ECX4 |
| C | Hydrolase | protein | 420 | 24% helix, 29% strand | B4ECX4 |
| D | Hydrolase | protein | 427 | 24% helix, 28% strand | B4ECX4 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1162 | 0.77 | 0.79 | 87 | EDO |
| 2 | 260 | 0.70 | 0.85 | 44 | SO4 |
| 3 | 185 | 0.69 | 0.87 | 36 | SO4 |
| 4 | 259 | 0.66 | 0.82 | 36 | SO4 |
| 5 | 244 | 0.65 | 0.83 | 45 | SO4 |
Interfaces
6 interfaces between chains.
- A–B · 2798 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 2752 Ų buried · 48 hydrogen bonds · protein-protein
- A–C · 317 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 149 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 47 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4QKU · Crystal structure of a putative hydrolase from Burkholderia cenocepacia · 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 B4ECX4
- Elsewhere: RCSB PDB 4QKU · PDBe 4QKU · UniProt B4ECX4
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