Research workbench
Crystal structure of S. aureus tari in complex with cdp-ribitol (space group P1211)
Analyse Crystal structure of S. aureus tari in complex with cdp-ribitol (space group… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XHT
- Type
- protein
- Length
- 1,407 residues
- Chains
- 6
- 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, SCN
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribitol-5-phosphate cytidylyltransferase 1 (EC 2.7.7.40) | protein | 233 | 40% helix, 26% strand | Q2G1C0 |
| B, C, D, F | Ribitol-5-phosphate cytidylyltransferase 1 (EC 2.7.7.40) | protein | 236 | 39% helix, 23% strand | Q2G1C0 |
| E | Ribitol-5-phosphate cytidylyltransferase 1 (EC 2.7.7.40) | protein | 230 | 40% helix, 23% strand | Q2G1C0 |
Ligands and binding sites
- V2V · CDP-ribitol · ligand · 2 copies · chains A, B, E, F
- SCN · Thiocyanate ion · ion · 11 copies · chains A, D, B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 926 | 0.82 | 0.84 | 95 | SCN |
| 2 | 985 | 0.81 | 0.82 | 91 | SCN |
| 3 | 711 | 0.79 | 0.84 | 75 | SCN |
| 4 | 634 | 0.67 | 0.77 | 61 | SCN |
| 5 | 262 | 0.55 | 0.77 | 36 | V2V |
Interfaces
9 interfaces between chains.
- E–F · 2123 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2107 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 2035 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 547 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 502 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6XHT · Crystal structure of S. aureus TarI in complex with CDP-ribitol (space group P1211) · the same entry in another collection · chain F against F, 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 E 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 6XHT · PDBe 6XHT · UniProt Q2G1C0
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