MolNFT v1 · #100606 · protein
Crystal structure of protein arginine deiminase 2 (D169A, 0 mm CA2+)
4N2F · Protein-arginine deiminase type-2: “Crystal structure of protein arginine deiminase 2 (D169A, 0 mm CA2+)”. X-ray diffraction, 1 ligand (CA), 5 pockets (best druggability 0.77). MolNFT v1 #100606 on GenesisL1: 3D structure, binding…
- PDB
- 4N2F
- Type
- protein
- Length
- 633 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
- 5 · best druggability 0.77
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 | 633 | 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 · 4 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.77 | 0.97 | 25 | CA |
| 2 | 362 | 0.67 | 0.81 | 51 | MPD |
| 3 | 92 | 0.38 | 0.76 | 16 | empty |
| 4 | 85 | 0.38 | 0.77 | 20 | empty |
| 5 | 72 | 0.31 | 0.74 | 20 | empty |
Compared structures
- 4N2F · Crystal structure of Protein Arginine Deiminase 2 (D169A, 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 4N2F · PDBe 4N2F · UniProt Q9Y2J8
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