Research workbench
Synthesis of CDP-activated ribitol for teichoic acid precursors in Streptococcus pneumoniae
Analyse Synthesis of CDP-activated ribitol for teichoic acid precursors in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VSI
- Type
- protein
- Length
- 452 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.75
- Source
- STREPTOCOCCUS PNEUMONIAE
- Molecule
- 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
- EC
- 2.7.7.60
- UniProt
- A5MSS9
- Ligands
- CDF, CA
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · resolution 2.75 · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC 2.7.7.60) | protein | 225 | 38% helix, 24% strand | A5MSS9 |
| B | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC 2.7.7.60) | protein | 227 | 39% helix, 24% strand | A5MSS9 |
Ligands and binding sites
- CDF · 4-amino-1-{5-O-[(R)-hydroxy(phosphonooxy)phosphoryl]-alpha-D-arabinofuranosyl}pyrimidin-2(1H)-one · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 915 | 0.75 | 0.79 | 69 | CDF |
| 2 | 303 | 0.60 | 0.79 | 43 | CDF |
Interfaces
1 interface between chains.
- A–B · 1612 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 2VSI · Synthesis of cdp-activated ribitol for teichoic acid precursors in streptococcus… · 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 A5MSS9
- Elsewhere: RCSB PDB 2VSI · PDBe 2VSI · UniProt A5MSS9
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