MolNFT v1 · #169613 · protein
Crystal structure of S. aureus tari in complex with cdp-ribitol (space group C121)
6XHQ · Ribitol-5-phosphate cytidylyltransferase 1: “Crystal structure of S. aureus tari in complex with cdp-ribitol (space group C121)”. X-ray diffraction, 1 ligand (V2V), 3 pockets (best druggability 0.85). MolNFT v1 #169613 on GenesisL1…
- PDB
- 6XHQ
- Type
- protein
- Length
- 465 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribitol-5-phosphate cytidylyltransferase 1
- EC
- 2.7.7.40
- UniProt
- Q2G1C0
- Ligands
- V2V
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribitol-5-phosphate cytidylyltransferase 1 (EC 2.7.7.40) | protein | 237 | 39% helix, 23% strand | Q2G1C0 |
| B | Ribitol-5-phosphate cytidylyltransferase 1 (EC 2.7.7.40) | protein | 228 | 40% helix, 24% strand | Q2G1C0 |
Ligands and binding sites
- V2V · CDP-ribitol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 369 | 0.85 | 0.93 | 33 | empty |
| 2 | 231 | 0.56 | 0.79 | 33 | V2V |
| 3 | 177 | 0.51 | 0.78 | 31 | V2V |
Interfaces
1 interface between chains.
- A–B · 2215 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 6XHQ · Crystal structure of S. aureus TarI in complex with CDP-ribitol (space group C121) · the same entry in another collection · chain A against A, TM-score 1.00
- Q2G1C0 · AlphaFold monomer V2.0 prediction for ribitol-5-phosphate cytidylyltransferase 1 (Q2G1C0) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q2G1C0
- Elsewhere: RCSB PDB 6XHQ · PDBe 6XHQ · UniProt Q2G1C0
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