Research workbench
X-ray crystal structure of cmp-kdo synthase from pseudomonas aeruginosa
Analyse X-ray crystal structure of cmp-kdo synthase from pseudomonas aeruginosa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XWI
- Type
- protein
- Length
- 479 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
- Q9HZM5
- Ligands
- NA, SO4
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-deoxy-manno-octulosonate cytidylyltransferase (EC 2.7.7.38) | protein | 252 | 35% helix, 22% strand | Q9HZM5 |
| B | 3-deoxy-manno-octulosonate cytidylyltransferase (EC 2.7.7.38) | protein | 227 | 33% helix, 23% strand | Q9HZM5 |
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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 524 | 0.63 | 0.76 | 47 | empty |
| 2 | 290 | 0.56 | 0.77 | 35 | empty |
| 3 | 58 | 0.37 | 0.79 | 16 | empty |
| 4 | 52 | 0.37 | 0.80 | 14 | empty |
| 5 | 52 | 0.35 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1443 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4XWI · X-ray Crystal structure of CMP-KDO Synthase from Pseudomonas aeruginosa · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HZM5 · AlphaFold monomer V2.0 prediction for 3-deoxy-manno-octulosonate cytidylyltransferase… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9HZM5
- Elsewhere: RCSB PDB 4XWI · PDBe 4XWI · UniProt Q9HZM5
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