Research workbench
The crystal structure of pyruvoyl-dependent arginine decarboxylase from methanococcus jannashii
Analyse The crystal structure of pyruvoyl-dependent arginine decarboxylase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1N13
- Type
- protein
- Length
- 949 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvoyl-dependent arginine decarboxylase beta chain; Pyruvoyl-dependent arginine…
- EC
- 4.1.1.19
- UniProt
- Q57764
- Ligands
- PYR, AG2
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 7 distinct chains · 24% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvoyl-dependent arginine decarboxylase beta chain (EC 4.1.1.19) | protein | 46 | 26% helix, 33% strand | Q57764 |
| B, D, F, H, J, L | Pyruvoyl-dependent arginine decarboxylase alpha chain (EC 4.1.1.19) | protein | 112 | 17% helix, 49% strand | Q57764 |
| C | Pyruvoyl-dependent arginine decarboxylase beta chain (EC 4.1.1.19) | protein | 48 | 31% helix, 31% strand | Q57764 |
| E | Pyruvoyl-dependent arginine decarboxylase beta chain (EC 4.1.1.19) | protein | 50 | 24% helix, 28% strand | Q57764 |
| G | Pyruvoyl-dependent arginine decarboxylase beta chain (EC 4.1.1.19) | protein | 41 | 29% helix, 37% strand | Q57764 |
| I | Pyruvoyl-dependent arginine decarboxylase beta chain (EC 4.1.1.19) | protein | 49 | 24% helix, 31% strand | Q57764 |
| K | Pyruvoyl-dependent arginine decarboxylase beta chain (EC 4.1.1.19) | protein | 43 | 28% helix, 35% strand | Q57764 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 6 copies · chains A, B, C, D, E, F, G, H, K, I, J, L
- AG2 · Agmatine · ligand · 6 copies · chains A, B, C, D, E, F, G, H, K, I, J, L
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 8 copies · chains A, B, E, C, D, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 751 | 0.77 | 0.81 | 81 | PYR, AG2, MRD |
| 2 | 876 | 0.75 | 0.79 | 76 | empty |
| 3 | 681 | 0.74 | 0.80 | 70 | PYR, MRD, AG2 |
| 4 | 65 | 0.70 | 0.96 | 17 | PYR, AG2 |
| 5 | 132 | 0.39 | 0.74 | 25 | empty |
Interfaces
33 interfaces between chains.
- I–J · 1956 Ų buried · 38 hydrogen bonds · protein-protein
- E–F · 1945 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 1912 Ų buried · 39 hydrogen bonds · protein-protein
- K–L · 1894 Ų buried · 38 hydrogen bonds · protein-protein
- G–H · 1816 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 1N13 · The Crystal Structure of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus… · the same entry in another collection · chain I against I, 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 1N13 · PDBe 1N13 · UniProt Q57764
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