Research workbench
Crystal structure of S. aureus tari in complex with CTP (space group P1211)
Analyse Crystal structure of S. aureus tari in complex with CTP (space group P1211) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XHS
- Type
- protein
- Length
- 1,394 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
- CTP, MG, SCN
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribitol-5-phosphate cytidylyltransferase 1 (EC 2.7.7.40) | protein | 234 | 39% helix, 25% strand | Q2G1C0 |
| B | Ribitol-5-phosphate cytidylyltransferase 1 (EC 2.7.7.40) | protein | 227 | 41% helix, 24% strand | Q2G1C0 |
| C | Ribitol-5-phosphate cytidylyltransferase 1 (EC 2.7.7.40) | protein | 236 | 39% helix, 25% strand | Q2G1C0 |
| D | Ribitol-5-phosphate cytidylyltransferase 1 (EC 2.7.7.40) | protein | 235 | 39% helix, 25% strand | Q2G1C0 |
| E | Ribitol-5-phosphate cytidylyltransferase 1 (EC 2.7.7.40) | protein | 232 | 39% helix, 23% strand | Q2G1C0 |
| F | Ribitol-5-phosphate cytidylyltransferase 1 (EC 2.7.7.40) | protein | 230 | 38% helix, 26% strand | Q2G1C0 |
Ligands and binding sites
- CTP · Cytidine-5'-triphosphate · ligand · 2 copies · chains B, E
- MG · Magnesium ion · metal
- SCN · Thiocyanate ion · ion · 2 copies · chains C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 927 | 0.79 | 0.81 | 90 | empty |
| 2 | 953 | 0.79 | 0.81 | 90 | SCN |
| 3 | 479 | 0.76 | 0.84 | 50 | empty |
| 4 | 472 | 0.68 | 0.80 | 49 | SCN |
| 5 | 488 | 0.67 | 0.78 | 51 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1964 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1851 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1849 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 528 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 492 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6XHS · Crystal structure of S. aureus TarI in complex with CTP (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 6XHS · PDBe 6XHS · UniProt Q2G1C0
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