Research workbench
The structure of CMP:2-keto-3-deoxy-manno-octonic acid synthetase and of its complexes with substrates and substrate analogues, CTP MG2+ complex
Analyse The structure of CMP:2-keto-3-deoxy-manno-octonic acid synthetase and of its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1H7G
- Type
- protein
- Length
- 486 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-deoxy-manno-octulosonate cytidylyltransferase
- EC
- 2.7.7.38
- UniProt
- P42216
- Ligands
- CTP, MG
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-deoxy-manno-octulosonate cytidylyltransferase (EC 2.7.7.38) | protein | 245 | 35% helix, 24% strand | P42216 |
| B | 3-deoxy-manno-octulosonate cytidylyltransferase (EC 2.7.7.38) | protein | 241 | 35% helix, 24% strand | P42216 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 583 | 0.65 | 0.76 | 45 | empty |
| 2 | 530 | 0.65 | 0.76 | 42 | MG, CTP |
| 3 | 189 | 0.55 | 0.79 | 20 | empty |
| 4 | 52 | 0.33 | 0.77 | 17 | empty |
| 5 | 53 | 0.33 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1396 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 1H7G · The structure of CMP:2-keto-3-deoxy-manno-octonic acid synthetase and of its complexes… · the same entry in another collection · chain A against A, TM-score 1.00
- P42216 · AlphaFold monomer V2.0 prediction for 3-deoxy-manno-octulosonate cytidylyltransferase… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P42216
- Elsewhere: RCSB PDB 1H7G · PDBe 1H7G · UniProt P42216
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