MolNFT v1 · #120930 · protein
Crystal structure of C-terminal domain of cargo proteins of type IX secretion system
5HFS · Gingipain R2: “Crystal structure of C-terminal domain of cargo proteins of type IX secretion system”. X-ray diffraction, 2 ligands (ZN, CA), 1 pocket (best druggability 0.47). MolNFT v1 #120930 on GenesisL1: 3D structure, binding…
- PDB
- 5HFS
- Type
- protein
- Length
- 130 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gingipain R2
- EC
- 3.4.22.37
- UniProt
- P95493
- Ligands
- ZN, CA
- Pockets
- 1 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 74% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Gingipain R2 (EC 3.4.22.37) | protein | 65 | 0% helix, 74% strand | P95493 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.47 | 0.85 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1437 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5HFS · Crystal structure of C-terminal domain of cargo proteins of type IX secretion system · 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 0.81
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 5HFS · PDBe 5HFS · UniProt P95493
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