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Crystal structure of phosphorylcholine esterase domain of the virulence factor choline binding protein E from streptococcus pneumoniae
Analyse Crystal structure of phosphorylcholine esterase domain of the virulence factor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WRA
- Type
- protein
- Length
- 613 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Teichoic acid phosphorylcholine ESTERASE/CHOLINE binding protein E (cbpe)
- EC
- 3.1.4.38
- UniProt
- Q8DQ62
- Ligands
- PC, FE, CA
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Teichoic acid phosphorylcholine ESTERASE/CHOLINE binding protein E (cbpe) (EC 3.1.4.38) | protein | 305 | 25% helix, 28% strand | Q8DQ62 |
| B | Teichoic acid phosphorylcholine ESTERASE/CHOLINE binding protein E (cbpe) (EC 3.1.4.38) | protein | 308 | 24% helix, 27% strand | Q8DQ62 |
Ligands and binding sites
- PC · Phosphocholine · ligand · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 699 | 0.71 | 0.78 | 49 | empty |
| 2 | 215 | 0.52 | 0.77 | 29 | PC |
| 3 | 238 | 0.51 | 0.76 | 29 | PC |
| 4 | 53 | 0.40 | 0.82 | 15 | empty |
| 5 | 63 | 0.35 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 351 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1WRA · Crystal Structure of Phosphorylcholine Esterase Domain of the Virulence Factor Choline… · 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 Q8DQ62
- Elsewhere: RCSB PDB 1WRA · PDBe 1WRA · UniProt Q8DQ62
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