Research workbench
Structural of pseudomonas aeruginosa dspi
Analyse Structural of pseudomonas aeruginosa dspi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WYD
- Type
- protein
- Length
- 1,572 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable enoyl-CoA HYDRATASE/ISOMERASE
- UniProt
- Q9I5I4
- Ligands
- PTD
- Pockets
- 16 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Probable enoyl-CoA HYDRATASE/ISOMERASE | protein | 262 | 49% helix, 16% strand | Q9I5I4 |
Ligands and binding sites
- PTD · Pentanedial · ligand · 3 copies · chains A, D, E
- IPA · Isopropyl alcohol · additive · 7 copies · chains B, C, F
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains B, C
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 853 | 0.80 | 0.82 | 105 | empty |
| 2 | 93 | 0.75 | 0.97 | 28 | empty |
| 3 | 104 | 0.74 | 0.95 | 29 | empty |
| 4 | 89 | 0.73 | 0.96 | 27 | empty |
| 5 | 347 | 0.72 | 0.84 | 50 | empty |
Interfaces
10 interfaces between chains.
- A–C · 2095 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 2081 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2007 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 365 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 288 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5WYD · Structural of Pseudomonas aeruginosa DspI · 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 Q9I5I4
- Elsewhere: RCSB PDB 5WYD · PDBe 5WYD · UniProt Q9I5I4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.