Research workbench
The crystal structure of SMU.793 from streptococcus mutans UA159 bound to acetyl CoA
Analyse The crystal structure of SMU.793 from streptococcus mutans UA159 bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LBE
- Type
- protein
- Length
- 491 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein SMU.793
- UniProt
- Q8DUV0
- Ligands
- COA, CL
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Putative uncharacterized protein SMU.793 | protein | 122 | 17% helix, 50% strand | Q8DUV0 |
| B | Putative uncharacterized protein SMU.793 | protein | 124 | 17% helix, 49% strand | Q8DUV0 |
| D | Putative uncharacterized protein SMU.793 | protein | 123 | 17% helix, 51% strand | Q8DUV0 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 4 copies · chains A, C, D, B
- CL · Chloride ion · ion · 4 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.74 | 0.87 | 41 | COA |
| 2 | 256 | 0.74 | 0.87 | 37 | COA |
| 3 | 271 | 0.73 | 0.87 | 41 | CL, COA |
| 4 | 275 | 0.73 | 0.86 | 41 | COA |
| 5 | 72 | 0.42 | 0.80 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1279 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1270 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 560 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 517 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 267 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3LBE · The Crystal Structure of smu.793 from Streptococcus mutans UA159 bound to acetyl CoA · 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 Q8DUV0
- Elsewhere: RCSB PDB 3LBE · PDBe 3LBE · UniProt Q8DUV0
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