Research workbench
Crystal structure of the nucleotide-binding domain of S. mutans coma, a bifunctional ATP-binding cassette transporter involved in the quorum-sensing pathway
Analyse Crystal structure of the nucleotide-binding domain of S. mutans coma, a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VX4
- Type
- protein
- Length
- 479 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
- Ligands
- ATP, MG
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative ABC transporter, ATP-binding protein coma | protein | 239 | 33% helix, 26% strand | Q8DW05 |
| D | Putative ABC transporter, ATP-binding protein coma | protein | 240 | 35% helix, 26% strand | Q8DW05 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, D
- MG · Magnesium ion · metal · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 992 | 0.79 | 0.81 | 124 | ATP, MG |
| 2 | 151 | 0.50 | 0.78 | 21 | empty |
| 3 | 158 | 0.47 | 0.77 | 28 | empty |
| 4 | 99 | 0.42 | 0.77 | 18 | empty |
| 5 | 79 | 0.37 | 0.77 | 11 | empty |
Interfaces
1 interface between chains.
- A–D · 974 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3VX4 · Crystal Structure of the Nucleotide-Binding Domain of S. mutans ComA, a Bifunctional… · 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 3VX4 · PDBe 3VX4 · UniProt Q8DW05
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