Research workbench
Crystal structure of human peptidylarginine deiminase 4 in complex with N-alpha-benzoyl-N5-(2-fluoro-1-iminoethyl)-L-ornithine amide
Analyse Crystal structure of human peptidylarginine deiminase 4 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DW5
- Type
- protein
- Length
- 626 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
- BFB, CA, SO4
- Pockets
- 5 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein-arginine deiminase type-4 (EC 3.5.3.15) | protein | 626 | 20% helix, 36% strand | Q9UM07 |
Ligands and binding sites
- BFB · N-[(1S)-1-(aminocarbonyl)-4-(ethanimidoylamino) butyl]benzamide · ligand · chains A
- CA · Calcium ion · metal · 5 copies · chains A
- SO4 · Sulfate ion · ion · 3 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.54 | 0.82 | 29 | BFB |
| 2 | 71 | 0.37 | 0.78 | 16 | empty |
| 3 | 51 | 0.37 | 0.80 | 15 | empty |
| 4 | 85 | 0.33 | 0.74 | 21 | empty |
| 5 | 50 | 0.30 | 0.77 | 12 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2DW5 · Crystal structure of human peptidylarginine deiminase 4 in complex with… · 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 2DW5 · PDBe 2DW5 · UniProt Q9UM07
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