Research workbench
Crystal structure of human peptidylarginine deiminase TYPE4 (PAD4) in complex with GSK199
Analyse Crystal structure of human peptidylarginine deiminase TYPE4 (PAD4) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X8G
- Type
- protein
- Length
- 606 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein-arginine deiminase type-4
- EC
- 3.5.3.15
- UniProt
- Q9UM07
- Ligands
- 3Z0, CA
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein-arginine deiminase type-4 (EC 3.5.3.15) | protein | 606 | 16% helix, 37% strand | Q9UM07 |
Ligands and binding sites
- 3Z0 · [(3R)-3-aminopiperidin-1-yl][2-(1-ethyl-1H-pyrrolo[2,3-b]pyridin-2-yl)-7-methoxy-1-methyl-1H-benzimidazol-5-yl]methanone · ligand · chains A
- CA · Calcium ion · metal · 4 copies · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.78 | 0.84 | 60 | CA, 3Z0 |
| 2 | 79 | 0.62 | 0.90 | 21 | empty |
| 3 | 95 | 0.55 | 0.84 | 21 | empty |
| 4 | 93 | 0.45 | 0.80 | 24 | empty |
| 5 | 55 | 0.27 | 0.73 | 18 | empty |
Compared structures
- 4X8G · Crystal structure of human peptidylarginine deiminase type4 (PAD4) in complex with GSK199 · 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 0.98
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 4X8G · PDBe 4X8G · UniProt Q9UM07
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