Research workbench
PADRON0.9-on (fluorescent state)
Analyse PADRON0.9-on (fluorescent state) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LS3
- Type
- protein
- Length
- 866 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PADRON0.9
- Ligands
- SPD, GYC
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PADRON0.9 | protein | 215 | 3% helix, 58% strand | — |
| B | PADRON0.9 | protein | 214 | 4% helix, 58% strand | — |
| C | PADRON0.9 | protein | 213 | 4% helix, 58% strand | — |
| D | PADRON0.9 | protein | 224 | 5% helix, 55% strand | — |
Ligands and binding sites
- SPD · Spermidine · ligand · 5 copies · chains A, B, C, D
- GYC · [(4Z)-2-[(1R)-1-amino-2-mercaptoethyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, C, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1067 | 0.83 | 0.84 | 94 | GOL, SPD |
| 2 | 83 | 0.76 | 0.99 | 27 | GYC |
| 3 | 71 | 0.74 | 0.98 | 27 | GYC |
| 4 | 69 | 0.74 | 0.98 | 24 | GYC |
| 5 | 61 | 0.71 | 0.98 | 23 | GYC |
Interfaces
4 interfaces between chains.
- A–B · 972 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 946 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 886 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 878 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 3LS3 · Padron0.9-ON (fluorescent state) · 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
- Elsewhere: RCSB PDB 3LS3 · PDBe 3LS3
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