MolNFT v1 · #52153 · protein
Synthesis of cdp-activated ribitol for teichoic acid precursors in streptococcus pneumoniae
2VSH · 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase: “Synthesis of cdp-activated ribitol for teichoic acid precursors in streptococcus pneumoniae”. X-ray diffraction, 1 ligand (CA), 2 pockets (best druggability 0.76). MolNFT v1…
- PDB
- 2VSH
- Type
- protein
- Length
- 445 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
- EC
- 2.7.7.60
- UniProt
- A5MSS9
- Ligands
- CA
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC 2.7.7.60) | protein | 223 | 43% helix, 25% strand | A5MSS9 |
| B | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC 2.7.7.60) | protein | 222 | 43% helix, 26% strand | A5MSS9 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains A
- P6G · Hexaethylene glycol · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 953 | 0.76 | 0.79 | 91 | empty |
| 2 | 108 | 0.36 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1563 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 2VSH · 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 2VSH · PDBe 2VSH · UniProt A5MSS9
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