Research workbench
Structure of the C646A mutant of peptidylarginine deiminase type III (PAD3)
Analyse Structure of the C646A mutant of peptidylarginine deiminase type III (PAD3) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D5V
- Type
- protein
- Length
- 1,240 residues
- Chains
- 2
- 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
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 17% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein-arginine deiminase type-3 (EC 3.5.3.15) | protein | 620 | 17% helix, 38% strand | Q9ULW8 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 25 copies · chains A, B
- GOL · Glycerol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 768 | 0.81 | 0.84 | 77 | EDO |
| 2 | 732 | 0.80 | 0.84 | 71 | EDO |
| 3 | 389 | 0.76 | 0.86 | 46 | empty |
| 4 | 425 | 0.75 | 0.85 | 56 | EDO |
| 5 | 330 | 0.67 | 0.82 | 34 | GOL |
Interfaces
1 interface between chains.
- A–B · 2993 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 7D5V · Structure of the C646A mutant of peptidylarginine deiminase type III (PAD3) · the same entry in another collection · chain A against A, 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 0.93
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 7D5V · PDBe 7D5V · UniProt Q9ULW8
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