MolNFT v1 · #34403 · protein
Crystal structure of human peptidylarginine deiminase 4 in complex with histone H4 N-terminal tail including ARG3
2DEY · Protein-arginine deiminase type IV: “Crystal structure of human peptidylarginine deiminase 4 in complex with histone H4 N-terminal tail including…”. X-ray diffraction, 3 ligands (ACE, CA, SO4), 4 pockets (best druggability 0.50).…
- PDB
- 2DEY
- Type
- protein
- Length
- 633 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein-arginine deiminase type IV; 10-mer peptide from histone H4
- EC
- 3.5.3.15
- UniProt
- Q9UM07
- Ligands
- ACE, CA, SO4
- Pockets
- 4 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Protein-arginine deiminase type IV (EC 3.5.3.15) | protein | 628 | 20% helix, 36% strand | Q9UM07 |
| A | 10-mer peptide from histone H4 | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains X, A
- CA · Calcium ion · metal · 5 copies · chains X
- SO4 · Sulfate ion · ion · 3 copies · chains X, A
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 | 68 | 0.50 | 0.85 | 21 | empty |
| 2 | 91 | 0.38 | 0.76 | 25 | empty |
| 3 | 69 | 0.34 | 0.76 | 14 | empty |
| 4 | 58 | 0.29 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- X–A · 382 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2DEY · Crystal structure of human peptidylarginine deiminase 4 in complex with histone H4… · the same entry in another collection · chain X against X, 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 X 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 2DEY · PDBe 2DEY · UniProt Q9UM07
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