MolNFT v1 · #117116 · protein
B. fragilis cysteine protease
5DYN · Putative peptidase: “B. fragilis cysteine protease”. X-ray diffraction, 2 ligands (NA, CL), 2 pockets (best druggability 0.52). MolNFT v1 #117116 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DYN
- Type
- protein
- Length
- 363 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative peptidase
- UniProt
- Q5LBR6
- Ligands
- NA, CL
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative peptidase | protein | 118 | 25% helix, 33% strand | Q5LBR6 |
| B | Putative peptidase | protein | 245 | 36% helix, 19% strand | Q5LBR6 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 128 | 0.52 | 0.81 | 29 | empty |
| 2 | 86 | 0.47 | 0.81 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2287 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 5DYN · B. fragilis cysteine protease · the same entry in another collection · chain A 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 Q5LBR6
- Elsewhere: RCSB PDB 5DYN · PDBe 5DYN · UniProt Q5LBR6
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