MolNFT v1 · #123885 · protein
Crystal structure of 3 mutant of BA3275 (S116A, E243A, H313A), the member of S66 family of serine peptidases
5JYB · Mccc family protein: “Crystal structure of 3 mutant of BA3275 (S116A, E243A, H313A), the member of S66 family of serine peptidases”. X-ray diffraction, 2 ligands (SBT, SO4), 7 pockets (best druggability 0.72). MolNFT v1 #123885 on…
- PDB
- 5JYB
- Type
- protein
- Length
- 688 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mccc family protein
- UniProt
- Q734X3
- Ligands
- SBT, SO4
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mccc family protein | protein | 344 | 36% helix, 22% strand | Q734X3 |
Ligands and binding sites
- SBT · 2-butanol · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- P6G · Hexaethylene glycol · additive · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains B
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 449 | 0.72 | 0.82 | 61 | SBT |
| 2 | 362 | 0.67 | 0.81 | 49 | EDO, SBT |
| 3 | 62 | 0.49 | 0.85 | 23 | empty |
| 4 | 62 | 0.48 | 0.85 | 15 | empty |
| 5 | 69 | 0.43 | 0.81 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1134 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5JYB · Crystal structure of 3 mutant of Ba3275 (S116A, E243A, H313A), the member of S66 family… · 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 Q734X3
- Elsewhere: RCSB PDB 5JYB · PDBe 5JYB · UniProt Q734X3
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