MolNFT v1 · #52359 · protein
Crystal structure of acid induced arginine decarboxylase from E. COLI
2VYC · Biodegradative arginine decarboxylase: “Crystal structure of acid induced arginine decarboxylase from E. COLI”. X-ray diffraction, 1 ligand (PLP), 20 pockets (best druggability 0.76). MolNFT v1 #52359 on GenesisL1: 3D structure…
- PDB
- 2VYC
- Type
- protein
- Length
- 7,550 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Biodegradative arginine decarboxylase
- EC
- 4.1.1.19
- UniProt
- P28629
- Ligands
- PLP
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Biodegradative arginine decarboxylase (EC 4.1.1.19) | protein | 755 | 42% helix, 16% strand | P28629 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 923 | 0.76 | 0.79 | 88 | empty |
| 2 | 958 | 0.76 | 0.79 | 96 | empty |
| 3 | 488 | 0.69 | 0.80 | 60 | empty |
| 4 | 475 | 0.69 | 0.80 | 59 | empty |
| 5 | 529 | 0.69 | 0.78 | 51 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1324 Ų buried · 15 hydrogen bonds · protein-protein
- F–J · 1303 Ų buried · 13 hydrogen bonds · protein-protein
- F–G · 1303 Ų buried · 17 hydrogen bonds · protein-protein
- I–J · 1303 Ų buried · 18 hydrogen bonds · protein-protein
- H–I · 1298 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 2VYC · Crystal Structure of Acid Induced Arginine Decarboxylase from E. coli · the same entry in another collection · chain J against J, TM-score 1.00
- P28629 · AlphaFold monomer V2.0 prediction for biodegradative arginine decarboxylase (P28629) · a predicted model of the same protein · chain I against A, TM-score 0.98
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 P28629
- Elsewhere: RCSB PDB 2VYC · PDBe 2VYC · UniProt P28629
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