MolNFT v1 · #89284 · protein
Crystal structure of human peptidylarginine deiminase 4 in complex with N-acetyl-L-threonyl-L-alpha-aspartyl-N5-[(1E)-2- fluoroethanimidoyl]-L-ornithinamide
4DKT · Protein-arginine deiminase type-4: “Crystal structure of human peptidylarginine deiminase 4 in complex with…”. X-ray diffraction, 4 ligands (FIO, CA, SO4), 5 pockets (best druggability 0.61). MolNFT v1 #89284 on GenesisL1: 3D…
- PDB
- 4DKT
- Type
- protein
- Length
- 637 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein-arginine deiminase type-4; Thr-asp-F-amidine
- EC
- 3.5.3.15
- UniProt
- Q9UM07
- Ligands
- FIO, CA, SO4, NH2
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein-arginine deiminase type-4 (EC 3.5.3.15) | protein | 636 | 21% helix, 36% strand | Q9UM07 |
| B | Thr-asp-F-amidine | protein | 1 | 0% helix, 0% strand | — |
Ligands and binding sites
- FIO · N~5~-[(1E)-2-fluoroethanimidoyl]-L-ornithine · ligand · chains A, B
- CA · Calcium ion · metal · 5 copies · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- NH2 · Amino group · ion · chains A, B
- EDO · 1,2-ethanediol · additive · 2 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 | 236 | 0.61 | 0.81 | 40 | FIO, NH2 |
| 2 | 89 | 0.40 | 0.77 | 26 | empty |
| 3 | 60 | 0.40 | 0.80 | 18 | empty |
| 4 | 54 | 0.32 | 0.77 | 15 | empty |
| 5 | 59 | 0.29 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 150 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4DKT · 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 4DKT · PDBe 4DKT · UniProt Q9UM07
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.