MolNFT v1 · #151882 · protein
Porphyromonas gingivalis peptidylarginine deminase (ppad) mutant G231N/E232T/N235D in complex with cl-amidine.
6I0X · Peptidylarginine deiminase: “Porphyromonas gingivalis peptidylarginine deminase (ppad) mutant G231N/E232T/N235D in complex with cl-amidine.”. X-ray diffraction, 2 ligands (BFB, NA), 7 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 6I0X
- Type
- protein
- Length
- 842 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidylarginine deiminase
- EC
- 3.5.3.-
- UniProt
- Q9RQJ2
- Ligands
- BFB, NA
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidylarginine deiminase (EC 3.5.3.-) | protein | 420 | 23% helix, 37% strand | Q9RQJ2 |
| B | Peptidylarginine deiminase (EC 3.5.3.-) | protein | 422 | 23% helix, 37% strand | Q9RQJ2 |
Ligands and binding sites
- BFB · N-[(1S)-1-(aminocarbonyl)-4-(ethanimidoylamino) butyl]benzamide · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1189 | 0.80 | 0.81 | 110 | GOL |
| 2 | 77 | 0.76 | 0.98 | 27 | empty |
| 3 | 69 | 0.74 | 0.98 | 25 | empty |
| 4 | 135 | 0.69 | 0.90 | 37 | empty |
| 5 | 119 | 0.68 | 0.90 | 37 | GOL |
Interfaces
1 interface between chains.
- A–B · 626 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6I0X · Porphyromonas gingivalis peptidylarginine deminase (PPAD) mutant G231N/E232T/N235D 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 B against A, TM-score 1.00
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 6I0X · PDBe 6I0X · UniProt Q9RQJ2
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