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The X-ray structure of CTP:INOSITOL-1-phosphate cytidylyltransferase from archaeoglobus fulgidus
Analyse The X-ray structure of CTP:INOSITOL-1-phosphate cytidylyltransferase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XMH
- Type
- protein
- Length
- 1,203 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CTP-inositol-1-phosphate cytidylyltransferase
- UniProt
- O29976
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 28% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CTP-inositol-1-phosphate cytidylyltransferase | protein | 196 | 30% helix, 32% strand | O29976 |
| B | CTP-inositol-1-phosphate cytidylyltransferase | protein | 196 | 29% helix, 32% strand | O29976 |
| C | CTP-inositol-1-phosphate cytidylyltransferase | protein | 201 | 27% helix, 31% strand | O29976 |
| D, E | CTP-inositol-1-phosphate cytidylyltransferase | protein | 205 | 28% helix, 31% strand | O29976 |
| F | CTP-inositol-1-phosphate cytidylyltransferase | protein | 200 | 28% helix, 30% strand | O29976 |
Ligands and binding sites
- FLC · Citrate anion · additive · 3 copies · chains A, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 429 | 0.74 | 0.83 | 59 | empty |
| 2 | 382 | 0.72 | 0.83 | 46 | empty |
| 3 | 300 | 0.66 | 0.81 | 50 | FLC |
| 4 | 303 | 0.63 | 0.80 | 43 | empty |
| 5 | 313 | 0.63 | 0.79 | 45 | FLC |
Interfaces
9 interfaces between chains.
- E–F · 1061 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 956 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 828 Ų buried · 13 hydrogen bonds · protein-protein
- B–E · 513 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 490 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2XMH · The X-ray structure of CTP:inositol-1-phosphate cytidylyltransferase from Archaeoglobus… · the same entry in another collection · chain F against F, TM-score 1.00
- O29976 · AlphaFold monomer V2.0 prediction for bifunctional ipc transferase and dipp synthase… · a predicted model of the same protein · chain A 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 O29976
- Elsewhere: RCSB PDB 2XMH · PDBe 2XMH · UniProt O29976
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