Research workbench
Calcium bound form of human peptidylarginine deiminase TYPE4 (PAD4)
Analyse Calcium bound form of human peptidylarginine deiminase TYPE4 (PAD4) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WD9
- Type
- protein
- Length
- 603 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein-arginine deiminase type IV
- EC
- 3.5.3.15
- UniProt
- Q9UM07
- Ligands
- CA, SO4
- Pockets
- 4 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein-arginine deiminase type IV (EC 3.5.3.15) | protein | 603 | 22% helix, 37% strand | Q9UM07 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.54 | 0.82 | 27 | empty |
| 2 | 80 | 0.36 | 0.76 | 24 | empty |
| 3 | 56 | 0.35 | 0.79 | 15 | empty |
| 4 | 56 | 0.29 | 0.75 | 17 | empty |
Compared structures
- 1WD9 · Calcium bound form of human peptidylarginine deiminase type4 (PAD4) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UM07 · AlphaFold monomer V2.0 prediction for protein-arginine deiminase type-4 (Q9UM07) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9UM07
- Elsewhere: RCSB PDB 1WD9 · PDBe 1WD9 · UniProt Q9UM07
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