MolNFT v1 · #49505 · protein
N47A mutant of pyruvoyl-dependent arginine decarboxylase from methanococcus jannashii
2QQD · Pyruvoyl-dependent arginine decarboxylase (ec 4.1.1.19)…: “N47A mutant of pyruvoyl-dependent arginine decarboxylase from methanococcus jannashii”. X-ray diffraction, 2 ligands (AG2, PYR), 5 pockets (best druggability 0.76). MolNFT…
- PDB
- 2QQD
- Type
- protein
- Length
- 935 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvoyl-dependent arginine decarboxylase (ec 4.1.1.19) (pvlargdc)
- EC
- 4.1.1.19
- UniProt
- Q57764
- Ligands
- AG2, PYR
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 20% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvoyl-dependent arginine decarboxylase (ec 4.1.1.19) (pvlargdc) (EC 4.1.1.19) | protein | 45 | 27% helix, 31% strand | Q57764 |
| B, E | Pyruvoyl-dependent arginine decarboxylase (ec 4.1.1.19) (pvlargdc) (EC 4.1.1.19) | protein | 112 | 17% helix, 49% strand | Q57764 |
| C | Pyruvoyl-dependent arginine decarboxylase (ec 4.1.1.19) (pvlargdc) (EC 4.1.1.19) | protein | 159 | 21% helix, 45% strand | Q57764 |
| D | Pyruvoyl-dependent arginine decarboxylase (ec 4.1.1.19) (pvlargdc) (EC 4.1.1.19) | protein | 50 | 24% helix, 30% strand | Q57764 |
| F, G | Pyruvoyl-dependent arginine decarboxylase (ec 4.1.1.19) (pvlargdc) (EC 4.1.1.19) | protein | 152 | 20% helix, 47% strand | Q57764 |
| H | Pyruvoyl-dependent arginine decarboxylase (ec 4.1.1.19) (pvlargdc) (EC 4.1.1.19) | protein | 153 | 19% helix, 46% strand | Q57764 |
Ligands and binding sites
- AG2 · Agmatine · ligand · 2 copies · chains A, D, E, B, C
- PYR · Pyruvic acid · ligand · 2 copies · chains A, B, D, E
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, C, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 865 | 0.76 | 0.79 | 76 | empty |
| 2 | 670 | 0.74 | 0.80 | 74 | AG2, PYR, MPD |
| 3 | 662 | 0.72 | 0.79 | 69 | empty |
| 4 | 182 | 0.48 | 0.75 | 14 | empty |
| 5 | 142 | 0.40 | 0.74 | 23 | empty |
Interfaces
15 interfaces between chains.
- D–E · 1903 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 1794 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 1012 Ų buried · 11 hydrogen bonds · protein-protein
- F–H · 850 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 836 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2QQD · N47A mutant of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannashii · the same entry in another collection · chain H against H, TM-score 1.00
- Q57764 · AlphaFold monomer V2.0 prediction for pyruvoyl-dependent arginine decarboxylase (Q57764) · a predicted model of the same protein · chain H 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 Q57764
- Elsewhere: RCSB PDB 2QQD · PDBe 2QQD · UniProt Q57764
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