MolNFT v1 · #70702 · protein
PADRON0.9-off (non-fluorescent state)
3LSA: “PADRON0.9-off (non-fluorescent state)”. X-ray diffraction, 3 ligands (GYC, SPD, SO4), 11 pockets (best druggability 0.83). MolNFT v1 #70702 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3LSA
- Type
- protein
- Length
- 863 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PADRON0.9
- Ligands
- GYC, SPD, SO4
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | PADRON0.9 | protein | 213 | 4% helix, 58% strand | — |
| D | PADRON0.9 | protein | 224 | 4% helix, 55% strand | — |
Ligands and binding sites
- 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
- SPD · Spermidine · ligand · 3 copies · chains A, B, D, C
- SO4 · Sulfate ion · ion · chains A, B
- GOL · Glycerol · additive · 4 copies · chains C, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1043 | 0.83 | 0.85 | 99 | SPD, EPE |
| 2 | 64 | 0.72 | 0.98 | 23 | GYC |
| 3 | 62 | 0.72 | 0.98 | 22 | GYC |
| 4 | 65 | 0.72 | 0.98 | 26 | GYC |
| 5 | 62 | 0.71 | 0.98 | 23 | GYC |
Interfaces
4 interfaces between chains.
- C–D · 927 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 899 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 895 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 879 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 3LSA · Padron0.9-OFF (non-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 3LSA · PDBe 3LSA
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