MolNFT v1 · #118313 · protein
LBCATS
5EY5 · Lbcats-a: “LBCATS”. X-ray diffraction, 3 ligands (G3P, PLP, NA), 10 pockets (best druggability 0.81). MolNFT v1 #118313 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5EY5
- Type
- protein
- Length
- 1,272 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lbcats-a; Lbca-B
- Ligands
- G3P, PLP, NA
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lbcats-a | protein | 261 | 47% helix, 13% strand | — |
| B, D | Lbca-B | protein | 383 | 50% helix, 20% strand | — |
| C | Lbcats-a | protein | 245 | 49% helix, 14% strand | — |
Ligands and binding sites
- G3P · Sn-glycerol-3-phosphate · ligand · 2 copies · chains A, C
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains B, D
- NA · Sodium ion · metal · 3 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 767 | 0.81 | 0.84 | 126 | PLP |
| 2 | 148 | 0.80 | 0.97 | 34 | PLP |
| 3 | 104 | 0.78 | 0.97 | 43 | G3P |
| 4 | 168 | 0.78 | 0.94 | 44 | G3P |
| 5 | 85 | 0.47 | 0.81 | 23 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1708 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1454 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1435 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5EY5 · LBCATS · 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 5EY5 · PDBe 5EY5
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