MolNFT v1 · #169615 · protein
Crystal structure of S. aureus tari in complex with CTP (space group P1211)
6XHS · Ribitol-5-phosphate cytidylyltransferase 1: “Crystal structure of S. aureus tari in complex with CTP (space group P1211)”. X-ray diffraction, 3 ligands (CTP, MG, SCN), 13 pockets (best druggability 0.79). MolNFT v1 #169615 on…
- 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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