MolNFT v1 · #109346 · protein
X-ray crystal structure of a putative aryl esterase from burkholderia cenocepacia
4X00 · Putative hydrolase: “X-ray crystal structure of a putative aryl esterase from burkholderia cenocepacia”. X-ray diffraction, 1 ligand (F), 7 pockets (best druggability 0.79). MolNFT v1 #109346 on GenesisL1: 3D structure, binding…
- PDB
- 4X00
- Type
- protein
- Length
- 1,090 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative hydrolase
- UniProt
- B4E794
- Ligands
- F
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Putative hydrolase | protein | 273 | 42% helix, 17% strand | B4E794 |
| B, D | Putative hydrolase | protein | 272 | 45% helix, 17% strand | B4E794 |
Ligands and binding sites
- F · Fluoride ion · ion · 3 copies · chains B, C, A, D
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, D, B, C
- GOL · Glycerol · additive · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 940 | 0.79 | 0.81 | 96 | EDO, F |
| 2 | 205 | 0.68 | 0.85 | 22 | empty |
| 3 | 228 | 0.68 | 0.84 | 23 | GOL |
| 4 | 229 | 0.67 | 0.84 | 24 | GOL |
| 5 | 176 | 0.63 | 0.84 | 23 | empty |
Interfaces
4 interfaces between chains.
- A–D · 923 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 343 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 198 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 175 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4X00 · X-ray crystal structure of a putative aryl esterase 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 B4E794
- Elsewhere: RCSB PDB 4X00 · PDBe 4X00 · UniProt B4E794
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