MolNFT v1 · #58379 · protein
Crystal structure of human peptidylarginine deiminase 4 in complex with O-F-amidine
3B1U · Protein-arginine deiminase type-4: “Crystal structure of human peptidylarginine deiminase 4 in complex with O-F-amidine”. X-ray diffraction, 3 ligands (YFF, CA, SO4), 5 pockets (best druggability 0.55). MolNFT v1 #58379 on…
- PDB
- 3B1U
- Type
- protein
- Length
- 628 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
- YFF, CA, SO4
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein-arginine deiminase type-4 (EC 3.5.3.15) | protein | 628 | 20% helix, 35% strand | Q9UM07 |
Ligands and binding sites
- YFF · 2-{[(2S)-1-amino-5-{[(1Z)-2-fluoroethanimidoyl]amino}-1-oxopentan-2-yl]carbamoyl}benzoic acid · 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 | 59 | 0.55 | 0.88 | 21 | empty |
| 2 | 100 | 0.38 | 0.75 | 26 | empty |
| 3 | 73 | 0.37 | 0.78 | 18 | YFF |
| 4 | 61 | 0.37 | 0.79 | 15 | empty |
| 5 | 56 | 0.36 | 0.79 | 15 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3B1U · Crystal structure of human peptidylarginine deiminase 4 in complex with o-F-amidine · 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 3B1U · PDBe 3B1U · UniProt Q9UM07
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