MolNFT v1 · #176073 · protein
Structure of the CA2+-bound wild-type peptidylarginine deiminase type III (PAD3)
7DAN · Protein-arginine deiminase type-3: “Structure of the CA2+-bound wild-type peptidylarginine deiminase type III (PAD3)”. X-ray diffraction, 2 ligands (CA, CL), 20 pockets (best druggability 0.71). MolNFT v1 #176073 on GenesisL1: 3D…
- PDB
- 7DAN
- Type
- protein
- Length
- 1,906 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein-arginine deiminase type-3
- EC
- 3.5.3.15
- UniProt
- Q9ULW8
- Ligands
- CA, CL
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Protein-arginine deiminase type-3 (EC 3.5.3.15) | protein | 636 | 17% helix, 34% strand | Q9ULW8 |
| B | Protein-arginine deiminase type-3 (EC 3.5.3.15) | protein | 635 | 17% helix, 33% strand | Q9ULW8 |
| A | Protein-arginine deiminase type-3 (EC 3.5.3.15) | protein | 635 | 17% helix, 34% strand | Q9ULW8 |
Ligands and binding sites
- CA · Calcium ion · metal · 15 copies · chains C, B, A
- CL · Chloride ion · ion · 11 copies · chains C, B, A
- EDO · 1,2-ethanediol · additive · 6 copies · chains C, B, A
- GOL · Glycerol · additive · 6 copies · chains C, B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 429 | 0.71 | 0.82 | 39 | GOL, CL |
| 2 | 417 | 0.70 | 0.81 | 38 | CL, GOL |
| 3 | 450 | 0.68 | 0.79 | 45 | empty |
| 4 | 489 | 0.68 | 0.78 | 53 | CL |
| 5 | 687 | 0.65 | 0.75 | 73 | EDO |
Interfaces
3 interfaces between chains.
- B–A · 1864 Ų buried · 14 hydrogen bonds · protein-protein
- C–A · 353 Ų buried · 10 hydrogen bonds · protein-protein
- C–B · 45 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7DAN · Structure of the Ca2+-bound wild-type peptidylarginine deiminase type III (PAD3) · the same entry in another collection · chain C against C, TM-score 1.00
- Q9ULW8 · AlphaFold monomer V2.0 prediction for protein-arginine deiminase type-3 (Q9ULW8) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9ULW8
- Elsewhere: RCSB PDB 7DAN · PDBe 7DAN · UniProt Q9ULW8
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