Research workbench
Crystal structure of the arg specific cysteine proteinase gingipain R (rgpb)
Analyse Crystal structure of the arg specific cysteine proteinase gingipain R (rgpb) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1CVR
- Type
- protein
- Length
- 432 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gingipain R
- EC
- 3.4.22.37
- UniProt
- P95493
- Ligands
- H37, CA, ZN
- Pockets
- 1 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gingipain R (EC 3.4.22.37) | protein | 432 | 30% helix, 27% strand | P95493 |
Ligands and binding sites
- H37 · D-phenylalanyl-N-[(3S)-6-carbamimidamido-1-chloro-2-oxohexan-3-yl]-L-phenylalaninamide · ligand · chains A
- CA · Calcium ion · metal · 6 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 301 | 0.68 | 0.83 | 34 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1CVR · Crystal structure of the Arg specific cysteine proteinase gingipain R (RGPB) · the same entry in another collection · chain A against A, TM-score 1.00
- P95493 · AlphaFold monomer V2.0 prediction for gingipain R2 (P95493) · 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 P95493
- Elsewhere: RCSB PDB 1CVR · PDBe 1CVR · UniProt P95493
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