MolNFT v1 · #111522 · protein
Crystal structure of porphyromonas gingivalis peptidylarginine deiminase (ppad) in complex with dipeptide asp-gln.
4YTB: “Crystal structure of porphyromonas gingivalis peptidylarginine deiminase (ppad) in complex with dipeptide…”. X-ray diffraction, 4 ligands (NA, PO4, CL), 3 pockets (best druggability 0.73). MolNFT v1 #111522 on GenesisL1: 3D…
- PDB
- 4YTB
- Type
- protein
- Length
- 424 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidylarginine deiminase
- EC
- 3.5.3.-
- UniProt
- Q9RQJ2
- Ligands
- NA, PO4, CL, AZI
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidylarginine deiminase (EC 3.5.3.-) | protein | 424 | 22% helix, 36% strand | Q9RQJ2 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- PO4 · Phosphate ion · ion · 5 copies · chains A
- CL · Chloride ion · ion
- AZI · Azide ion · ion · chains A
- GOL · Glycerol · additive · 3 copies · chains A
- IMD · Imidazole · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.73 | 0.98 | 27 | empty |
| 2 | 139 | 0.66 | 0.88 | 38 | empty |
| 3 | 97 | 0.40 | 0.77 | 19 | empty |
Compared structures
- 4YTB · Crystal structure of Porphyromonas gingivalis peptidylarginine deiminase (PPAD) in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9RQJ2 · AlphaFold monomer V2.0 prediction for peptidylarginine deiminase (Q9RQJ2) · 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 Q9RQJ2
- Elsewhere: RCSB PDB 4YTB · PDBe 4YTB · UniProt Q9RQJ2
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