MolNFT v1 · #111520 · protein
Crystal structure of porphyromonas gingivalis peptidylarginine deiminase (ppad) substrate-unbound.
4YT9: “Crystal structure of porphyromonas gingivalis peptidylarginine deiminase (ppad) substrate-unbound.”. X-ray diffraction, 1 ligand (NA), 4 pockets (best druggability 0.73). MolNFT v1 #111520 on GenesisL1: 3D structure, binding sites…
- PDB
- 4YT9
- Type
- protein
- Length
- 421 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
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidylarginine deiminase (EC 3.5.3.-) | protein | 421 | 23% helix, 35% strand | Q9RQJ2 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.73 | 0.98 | 27 | empty |
| 2 | 196 | 0.70 | 0.87 | 39 | GOL |
| 3 | 52 | 0.50 | 0.87 | 17 | GOL |
| 4 | 87 | 0.42 | 0.78 | 14 | GOL |
Modifications
Observed in the structure: 3 modified (nonstandard).
Compared structures
- 4YT9 · Crystal structure of Porphyromonas gingivalis peptidylarginine deiminase (PPAD)… · 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 4YT9 · PDBe 4YT9 · UniProt Q9RQJ2
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