MolNFT v1 · #119923 · protein
Crystal structure of srldc in complex with plp and cadaverine
5GJP · LYSINE/ORNITHINE decarboxylase: “Crystal structure of srldc in complex with plp and cadaverine”. X-ray diffraction, 4 ligands (N2P, PLP, NA), 3 pockets (best druggability 0.53). MolNFT v1 #119923 on GenesisL1: 3D structure, binding…
- PDB
- 5GJP
- Type
- protein
- Length
- 381 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LYSINE/ORNITHINE decarboxylase
- EC
- 4.1.1.18
- UniProt
- O50657
- Ligands
- N2P, PLP, NA, MG
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LYSINE/ORNITHINE decarboxylase (EC 4.1.1.18) | protein | 381 | 38% helix, 21% strand | O50657 |
Ligands and binding sites
- N2P · Pentane-1,5-diamine · ligand · chains A
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.53 | 0.78 | 34 | N2P, PLP |
| 2 | 89 | 0.48 | 0.81 | 17 | PGE |
| 3 | 86 | 0.38 | 0.76 | 14 | GOL |
Compared structures
- 5GJP · Crystal structure of SrLDC in complex with PLP and Cadaverine · 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 A against A, TM-score 0.99
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 5GJP · PDBe 5GJP · UniProt O50657
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