Research workbench
Crystal structure of E. COLI lipopolysaccharide specific cmp-kdo synthetase
Analyse Crystal structure of E. COLI lipopolysaccharide specific cmp-kdo synthetase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K8E
- Type
- protein
- Length
- 970 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-deoxy-manno-octulosonate cytidylyltransferase
- EC
- 2.7.7.38
- UniProt
- P04951
- Pockets
- 12 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 3-deoxy-manno-octulosonate cytidylyltransferase (EC 2.7.7.38) | protein | 244 | 34% helix, 22% strand | P04951 |
| D | 3-deoxy-manno-octulosonate cytidylyltransferase (EC 2.7.7.38) | protein | 238 | 33% helix, 23% strand | P04951 |
| A | 3-deoxy-manno-octulosonate cytidylyltransferase (EC 2.7.7.38) | protein | 242 | 33% helix, 23% strand | P04951 |
| B | 3-deoxy-manno-octulosonate cytidylyltransferase (EC 2.7.7.38) | protein | 246 | 35% helix, 23% strand | P04951 |
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 458 | 0.69 | 0.80 | 46 | empty |
| 2 | 519 | 0.65 | 0.77 | 41 | empty |
| 3 | 533 | 0.65 | 0.76 | 42 | empty |
| 4 | 89 | 0.64 | 0.90 | 18 | empty |
| 5 | 390 | 0.63 | 0.78 | 40 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1172 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1087 Ų buried · 7 hydrogen bonds · protein-protein
- C–B · 185 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3K8E · Crystal structure of E. coli lipopolysaccharide specific CMP-KDO synthetase · the same entry in another collection · chain B against B, TM-score 1.00
- P04951 · AlphaFold monomer V2.0 prediction for 3-deoxy-manno-octulosonate cytidylyltransferase… · a predicted model of the same protein · chain D 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 P04951
- Elsewhere: RCSB PDB 3K8E · PDBe 3K8E · UniProt P04951
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