Research workbench
Crystal structure of biosynthetic arginine decarboxylase adc (spea) from escherichia COLI, northeast structural genomics consortium target ER600
Analyse Crystal structure of biosynthetic arginine decarboxylase adc (spea) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NZQ
- Type
- protein
- Length
- 1,256 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Biosynthetic arginine decarboxylase
- EC
- 4.1.1.19
- UniProt
- P21170
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Biosynthetic arginine decarboxylase (EC 4.1.1.19) | protein | 628 | 40% helix, 17% strand | P21170 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 203 | 0.58 | 0.80 | 42 | SO4 |
| 2 | 202 | 0.57 | 0.80 | 44 | SO4 |
| 3 | 63 | 0.48 | 0.84 | 16 | empty |
| 4 | 54 | 0.46 | 0.85 | 18 | empty |
| 5 | 89 | 0.34 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 92 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3NZQ · Crystal Structure of Biosynthetic arginine decarboxylase ADC (SpeA) from Escherichia… · the same entry in another collection · chain A against A, TM-score 1.00
- P21170 · AlphaFold monomer V2.0 prediction for biosynthetic arginine decarboxylase (P21170) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P21170
- Elsewhere: RCSB PDB 3NZQ · PDBe 3NZQ · UniProt P21170
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