MolNFT v1 · #100597 · protein
Crystal structure of protein arginine deiminase 2 (250 um CA2+)
4N25 · Protein-arginine deiminase type-2: “Crystal structure of protein arginine deiminase 2 (250 um CA2+)”. X-ray diffraction, 1 ligand (CA), 6 pockets (best druggability 0.78). MolNFT v1 #100597 on GenesisL1: 3D structure, binding sites…
- PDB
- 4N25
- Type
- protein
- Length
- 638 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 0.78
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein-arginine deiminase type-2 (EC 3.5.3.15) | protein | 638 | 19% helix, 36% strand | Q9Y2J8 |
Ligands and binding sites
- CA · Calcium ion · metal · 5 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 394 | 0.78 | 0.87 | 62 | MPD |
| 2 | 76 | 0.38 | 0.77 | 15 | empty |
| 3 | 108 | 0.37 | 0.74 | 22 | empty |
| 4 | 86 | 0.34 | 0.74 | 19 | empty |
| 5 | 70 | 0.30 | 0.74 | 20 | empty |
Compared structures
- 4N25 · Crystal structure of Protein Arginine Deiminase 2 (250 uM 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 0.98
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 Q9Y2J8
- Elsewhere: RCSB PDB 4N25 · PDBe 4N25 · UniProt Q9Y2J8
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