Research workbench
Crystal structure of the peptidase domain of streptococcus mutans coma
Analyse Crystal structure of the peptidase domain of streptococcus mutans coma in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XE8
- Type
- protein
- Length
- 257 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative ABC transporter, ATP-binding protein coma
- UniProt
- Q8DW05
- Pockets
- 4 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative ABC transporter, ATP-binding protein coma | protein | 135 | 29% helix, 36% strand | Q8DW05 |
| C | Putative ABC transporter, ATP-binding protein coma | protein | 122 | 27% helix, 39% strand | Q8DW05 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.47 | 0.77 | 19 | empty |
| 2 | 56 | 0.45 | 0.84 | 21 | empty |
| 3 | 58 | 0.44 | 0.84 | 18 | empty |
| 4 | 76 | 0.41 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–C · 1025 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5XE8 · Crystal Structure of the Peptidase Domain of Streptococcus mutans ComA · 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 Q8DW05
- Elsewhere: RCSB PDB 5XE8 · PDBe 5XE8 · UniProt Q8DW05
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