MolNFT v1 · #52369 · protein
Crystal structure of choline binding protein F from streptococcus pneumoniae in the presence of a peptidoglycan analogue (tetrasaccharide-pentapeptide)
2VYU: “Crystal structure of choline binding protein F from streptococcus pneumoniae in the presence of a…”. X-ray diffraction, 1 ligand (CHT), 3 pockets (best druggability 0.38). MolNFT v1 #52369 on GenesisL1: 3D structure, binding sites…
- PDB
- 2VYU
- Type
- protein
- Length
- 300 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Choline binding protein F
- UniProt
- Q8DR52
- Ligands
- CHT
- Pockets
- 3 · best druggability 0.38
Structure
x-ray diffraction · 1 distinct chain · 1% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Choline binding protein F | protein | 300 | 1% helix, 45% strand | Q8DR52 |
Ligands and binding sites
- CHT · Choline ion · ligand · 7 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.38 | 0.79 | 20 | empty |
| 2 | 52 | 0.30 | 0.75 | 16 | empty |
| 3 | 79 | 0.28 | 0.71 | 20 | empty |
Compared structures
- 2VYU · Crystal structure of choline binding protein F from streptococcus pneumoniae in the… · 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 Q8DR52
- Elsewhere: RCSB PDB 2VYU · PDBe 2VYU · UniProt Q8DR52
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