MolNFT v1 · #63893 · protein
Crystal structure of acylaminoacyl peptidase SMU_737 from streptococcus mutans UA159
3FNB: “Crystal structure of acylaminoacyl peptidase SMU_737 from streptococcus mutans UA159”. X-ray diffraction, 1 ligand (MG), 9 pockets (best druggability 0.80). MolNFT v1 #63893 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3FNB
- Type
- protein
- Length
- 745 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acylaminoacyl peptidase SMU_737
- UniProt
- Q8DUZ1
- Ligands
- MG
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acylaminoacyl peptidase SMU_737 | protein | 374 | 53% helix, 13% strand | Q8DUZ1 |
| B | Acylaminoacyl peptidase SMU_737 | protein | 371 | 53% helix, 13% strand | Q8DUZ1 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 455 | 0.80 | 0.87 | 56 | BME, PGE |
| 2 | 644 | 0.78 | 0.83 | 59 | BME, PGE, EDO |
| 3 | 72 | 0.76 | 1.00 | 17 | empty |
| 4 | 64 | 0.73 | 0.99 | 17 | empty |
| 5 | 721 | 0.71 | 0.77 | 44 | empty |
Interfaces
1 interface between chains.
- A–B · 1744 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3FNB · Crystal structure of acylaminoacyl peptidase SMU_737 from Streptococcus mutans UA159 · 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 Q8DUZ1
- Elsewhere: RCSB PDB 3FNB · PDBe 3FNB · UniProt Q8DUZ1
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