MolNFT v1 · #111527 · protein
Crystal structure of porphyromonas gingivalis peptidylarginine deiminase (ppad) mutant C351A in complex with dipeptide met-arg.
4YTG: “Crystal structure of porphyromonas gingivalis peptidylarginine deiminase (ppad) mutant C351A in complex with…”. X-ray diffraction, 3 ligands (NA, AZI, CL), 3 pockets (best druggability 0.76). MolNFT v1 #111527 on GenesisL1: 3D…
- PDB
- 4YTG
- Type
- protein
- Length
- 419 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, AZI, CL
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidylarginine deiminase (EC 3.5.3.-) | protein | 419 | 23% helix, 37% strand | Q9RQJ2 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- AZI · Azide ion · ion · 2 copies · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 5 copies · 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 | 73 | 0.76 | 0.99 | 28 | empty |
| 2 | 149 | 0.67 | 0.88 | 40 | GOL, AZI |
| 3 | 95 | 0.38 | 0.76 | 20 | GOL |
Compared structures
- 4YTG · Crystal structure of Porphyromonas gingivalis peptidylarginine deiminase (PPAD) mutant… · 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 4YTG · PDBe 4YTG · UniProt Q9RQJ2
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