MolNFT v1 · #119922 · protein
Crystal structure of srldc mutant (A225C/T302C) in complex with plp
5GJO · LYSINE/ORNITHINE decarboxylase: “Crystal structure of srldc mutant (A225C/T302C) in complex with plp”. X-ray diffraction, 3 ligands (PLP, NA, SO4), 11 pockets (best druggability 0.78). MolNFT v1 #119922 on GenesisL1: 3D structure…
- PDB
- 5GJO
- Type
- protein
- Length
- 769 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LYSINE/ORNITHINE decarboxylase
- EC
- 4.1.1.18
- UniProt
- O50657
- Ligands
- PLP, NA, SO4
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LYSINE/ORNITHINE decarboxylase (EC 4.1.1.18) | protein | 385 | 38% helix, 23% strand | O50657 |
| B | LYSINE/ORNITHINE decarboxylase (EC 4.1.1.18) | protein | 384 | 38% helix, 23% strand | O50657 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.78 | 0.97 | 34 | PLP |
| 2 | 106 | 0.77 | 0.97 | 31 | PLP |
| 3 | 67 | 0.66 | 0.94 | 28 | empty |
| 4 | 59 | 0.63 | 0.93 | 28 | empty |
| 5 | 389 | 0.60 | 0.76 | 44 | GOL |
Interfaces
1 interface between chains.
- A–B · 2720 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5GJO · Crystal structure of SrLDC mutant (A225C/T302C) in complex with PLP · the same entry in another collection · chain A against A, TM-score 1.00
- O50657 · AlphaFold monomer V2.0 prediction for LYSINE/ORNITHINE decarboxylase (O50657) · a predicted model of the same protein · chain B 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 O50657
- Elsewhere: RCSB PDB 5GJO · PDBe 5GJO · UniProt O50657
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