MolNFT v1 · #140009 · protein
Crystal structure of arginine decarboxylase (adia) from salmonella typhimurium
5XX1: “Crystal structure of arginine decarboxylase (adia) from salmonella typhimurium”. X-ray diffraction, 1 ligand (PO4), 20 pockets (best druggability 0.82). MolNFT v1 #140009 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5XX1
- Type
- protein
- Length
- 7,330 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginine decarboxylase
- EC
- 4.1.1.19
- UniProt
- Q8Z1P1
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 10 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arginine decarboxylase (EC 4.1.1.19) | protein | 733 | 44% helix, 17% strand | Q8Z1P1 |
| B | Arginine decarboxylase (EC 4.1.1.19) | protein | 732 | 45% helix, 17% strand | Q8Z1P1 |
| C | Arginine decarboxylase (EC 4.1.1.19) | protein | 733 | 44% helix, 17% strand | Q8Z1P1 |
| D | Arginine decarboxylase (EC 4.1.1.19) | protein | 731 | 45% helix, 17% strand | Q8Z1P1 |
| E | Arginine decarboxylase (EC 4.1.1.19) | protein | 732 | 44% helix, 17% strand | Q8Z1P1 |
| F | Arginine decarboxylase (EC 4.1.1.19) | protein | 732 | 45% helix, 16% strand | Q8Z1P1 |
| G | Arginine decarboxylase (EC 4.1.1.19) | protein | 735 | 45% helix, 17% strand | Q8Z1P1 |
| H | Arginine decarboxylase (EC 4.1.1.19) | protein | 733 | 45% helix, 17% strand | Q8Z1P1 |
| I | Arginine decarboxylase (EC 4.1.1.19) | protein | 735 | 44% helix, 17% strand | Q8Z1P1 |
| J | Arginine decarboxylase (EC 4.1.1.19) | protein | 734 | 44% helix, 17% strand | Q8Z1P1 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 10 copies · chains A, J, B, I, C, H, D, G, E, F
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 | 963 | 0.82 | 0.83 | 113 | empty |
| 2 | 818 | 0.80 | 0.83 | 103 | PO4 |
| 3 | 1151 | 0.79 | 0.81 | 116 | empty |
| 4 | 1082 | 0.79 | 0.81 | 107 | empty |
| 5 | 1150 | 0.79 | 0.81 | 124 | empty |
Interfaces
20 interfaces between chains.
- A–J · 4463 Ų buried · 65 hydrogen bonds · protein-protein
- D–G · 4321 Ų buried · 57 hydrogen bonds · protein-protein
- C–H · 4284 Ų buried · 56 hydrogen bonds · protein-protein
- E–F · 4095 Ų buried · 52 hydrogen bonds · protein-protein
- B–I · 4095 Ų buried · 56 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (artifact).
Compared structures
- 5XX1 · Crystal structure of Arginine decarboxylase (AdiA) from Salmonella typhimurium · 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 Q8Z1P1
- Elsewhere: RCSB PDB 5XX1 · PDBe 5XX1 · UniProt Q8Z1P1
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