MolNFT v1 · #73361 · protein
Crystal structure of the biosynthetic arginine decarboxylase spea from campylobacter jejuni, northeast structural genomics consortium target BR53
3NZP: “Crystal structure of the biosynthetic arginine decarboxylase spea from campylobacter jejuni, northeast…”. X-ray diffraction, 2 ligands (PLP, SO4), 9 pockets (best druggability 0.76). MolNFT v1 #73361 on GenesisL1: 3D structure…
- PDB
- 3NZP
- Type
- protein
- Length
- 1,174 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginine decarboxylase
- EC
- 4.1.1.19
- UniProt
- Q0PAC6
- Ligands
- PLP, SO4
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arginine decarboxylase (EC 4.1.1.19) | protein | 583 | 40% helix, 17% strand | Q0PAC6 |
| B | Arginine decarboxylase (EC 4.1.1.19) | protein | 591 | 40% helix, 16% strand | Q0PAC6 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 709 | 0.76 | 0.81 | 99 | PLP |
| 2 | 503 | 0.73 | 0.82 | 56 | empty |
| 3 | 337 | 0.69 | 0.83 | 50 | PLP |
| 4 | 360 | 0.60 | 0.77 | 47 | empty |
| 5 | 91 | 0.55 | 0.85 | 21 | SO4 |
Interfaces
1 interface between chains.
- A–B · 6159 Ų buried · 62 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3NZP · Crystal Structure of the Biosynthetic Arginine decarboxylase SpeA from Campylobacter… · 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 Q0PAC6
- Elsewhere: RCSB PDB 3NZP · PDBe 3NZP · UniProt Q0PAC6
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