MolNFT v1 · #72231 · protein
Crystal structure of carboxynorspermidine decarboxylase complexed with norspermidine from campylobacter jejuni
3N29: “Crystal structure of carboxynorspermidine decarboxylase complexed with norspermidine from campylobacter jejuni”. X-ray diffraction, 2 ligands (PLP, NSD), 7 pockets (best druggability 0.72). MolNFT v1 #72231 on GenesisL1: 3D…
- PDB
- 3N29
- Type
- protein
- Length
- 738 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxynorspermidine decarboxylase
- UniProt
- A3ZCM2
- Ligands
- PLP, NSD
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carboxynorspermidine decarboxylase | protein | 371 | 32% helix, 25% strand | A3ZCM2 |
| B | Carboxynorspermidine decarboxylase | protein | 367 | 32% helix, 26% strand | A3ZCM2 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- NSD · N-(3-aminopropyl)propane-1,3-diamine · ligand · 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
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 595 | 0.72 | 0.80 | 74 | PLP, GOL |
| 2 | 628 | 0.72 | 0.79 | 79 | PLP, NSD, GOL |
| 3 | 95 | 0.39 | 0.77 | 18 | empty |
| 4 | 77 | 0.39 | 0.77 | 12 | empty |
| 5 | 50 | 0.37 | 0.81 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 3877 Ų buried · 70 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 3N29 · Crystal structure of carboxynorspermidine decarboxylase complexed with Norspermidine from… · 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
- Every structure of UniProt A3ZCM2
- Elsewhere: RCSB PDB 3N29 · PDBe 3N29 · UniProt A3ZCM2
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