Research workbench
Crystal structure of 3-deoxy-manno-octulosonate cytidylyltransferase from haemophilus influenzae complexed with the substrate 3-deoxy- manno-octulosonate in the-configuration
Analyse Crystal structure of 3-deoxy-manno-octulosonate cytidylyltransferase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DUV
- Type
- protein
- Length
- 492 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
- P44490
- Ligands
- KDO
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-deoxy-manno-octulosonate cytidylyltransferase (EC 2.7.7.38) | protein | 238 | 34% helix, 22% strand | P44490 |
| B | 3-deoxy-manno-octulosonate cytidylyltransferase (EC 2.7.7.38) | protein | 254 | 36% helix, 23% strand | P44490 |
Ligands and binding sites
- KDO · 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid · sugar · 2 copies · chains A, B
- P4C · O-acetaldehydyl-hexaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 484 | 0.78 | 0.86 | 46 | KDO |
| 2 | 181 | 0.61 | 0.83 | 18 | empty |
| 3 | 135 | 0.49 | 0.78 | 23 | empty |
| 4 | 172 | 0.47 | 0.76 | 22 | empty |
| 5 | 134 | 0.46 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1485 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 3DUV · Crystal structure of 3-deoxy-manno-octulosonate cytidylyltransferase from Haemophilus… · the same entry in another collection · chain A against A, TM-score 1.00
- P44490 · AlphaFold monomer V2.0 prediction for 3-deoxy-manno-octulosonate cytidylyltransferase… · a predicted model of the same protein · chain B against A, TM-score 0.89
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 P44490
- Elsewhere: RCSB PDB 3DUV · PDBe 3DUV · UniProt P44490
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