MolNFT v1 · #100592 · protein
Crystal structure of protein arginine deiminase 2 (0 mm CA2+)
4N20 · Protein-arginine deiminase type-2: “Crystal structure of protein arginine deiminase 2 (0 mm CA2+)”. X-ray diffraction, 1 ligand (CA), 6 pockets (best druggability 0.81). MolNFT v1 #100592 on GenesisL1: 3D structure, binding sites…
- PDB
- 4N20
- Type
- protein
- Length
- 639 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein-arginine deiminase type-2
- EC
- 3.5.3.15
- UniProt
- Q9Y2J8
- Ligands
- CA
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein-arginine deiminase type-2 (EC 3.5.3.15) | protein | 639 | 18% helix, 37% strand | Q9Y2J8 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 162 | 0.81 | 0.97 | 26 | CA |
| 2 | 269 | 0.64 | 0.81 | 45 | empty |
| 3 | 83 | 0.41 | 0.78 | 16 | MPD |
| 4 | 116 | 0.38 | 0.75 | 25 | empty |
| 5 | 74 | 0.34 | 0.75 | 13 | empty |
Compared structures
- 4N20 · Crystal structure of Protein Arginine Deiminase 2 (0 mM Ca2+) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y2J8 · AlphaFold monomer V2.0 prediction for protein-arginine deiminase type-2 (Q9Y2J8) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9Y2J8
- Elsewhere: RCSB PDB 4N20 · PDBe 4N20 · UniProt Q9Y2J8
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