Research workbench
Crystal structure of the biosynthetic arginine decarboxylase spea from campylobacter jejuni, northeast structural genomics consortium target BR53
Analyse Crystal structure of the biosynthetic arginine decarboxylase spea from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 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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