Research workbench
Structure of the inactive form of wild-type peptidylarginine deiminase type III (PAD3) crystallized under the condition with high concentrations of CA2+
Analyse Structure of the inactive form of wild-type peptidylarginine deiminase type III… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D8N
- Type
- protein
- Length
- 1,253 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
- Ligands
- CA, CL
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein-arginine deiminase type-3 (EC 3.5.3.15) | protein | 625 | 18% helix, 36% strand | Q9ULW8 |
| B | Protein-arginine deiminase type-3 (EC 3.5.3.15) | protein | 628 | 18% helix, 36% strand | Q9ULW8 |
Ligands and binding sites
- CA · Calcium ion · metal · 10 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.79 | 0.96 | 25 | empty |
| 2 | 935 | 0.78 | 0.81 | 88 | GOL |
| 3 | 941 | 0.78 | 0.81 | 89 | GOL |
| 4 | 413 | 0.75 | 0.85 | 51 | CA |
| 5 | 307 | 0.62 | 0.79 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 2765 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 7D8N · Structure of the inactive form of wild-type 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 0.97
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 Q9ULW8
- Elsewhere: RCSB PDB 7D8N · PDBe 7D8N · UniProt Q9ULW8
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