MolNFT v1 · #169614 · protein
Crystal structure of S. aureus tari (space group P1211)
6XHR · Ribitol-5-phosphate cytidylyltransferase 1: “Crystal structure of S. aureus tari (space group P1211)”. X-ray diffraction, 1 ligand (SCN), 14 pockets (best druggability 0.79). MolNFT v1 #169614 on GenesisL1: 3D structure, binding…
- PDB
- 6XHR
- Type
- protein
- Length
- 1,389 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
- SCN
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Ribitol-5-phosphate cytidylyltransferase 1 (EC 2.7.7.40) | protein | 236 | 39% helix, 25% strand | Q2G1C0 |
| B | Ribitol-5-phosphate cytidylyltransferase 1 (EC 2.7.7.40) | protein | 222 | 42% helix, 25% strand | Q2G1C0 |
| E | Ribitol-5-phosphate cytidylyltransferase 1 (EC 2.7.7.40) | protein | 226 | 41% helix, 24% strand | Q2G1C0 |
| F | Ribitol-5-phosphate cytidylyltransferase 1 (EC 2.7.7.40) | protein | 233 | 40% helix, 25% strand | Q2G1C0 |
Ligands and binding sites
- SCN · Thiocyanate ion · ion · 8 copies · chains A, D, C, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 892 | 0.79 | 0.81 | 84 | SCN |
| 2 | 1057 | 0.79 | 0.81 | 103 | SCN |
| 3 | 325 | 0.74 | 0.86 | 43 | empty |
| 4 | 360 | 0.68 | 0.82 | 44 | SCN |
| 5 | 362 | 0.65 | 0.80 | 46 | SCN |
Interfaces
9 interfaces between chains.
- C–D · 1914 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1902 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1716 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 537 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 527 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6XHR · Crystal structure of S. aureus TarI (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 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 6XHR · PDBe 6XHR · UniProt Q2G1C0
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