Research workbench
Crystal structure of E. COLI lipopolysaccharide specific cmp-kdo synthetase in complex with CTP and 2-deoxy-kdo
Analyse Crystal structure of E. COLI lipopolysaccharide specific cmp-kdo synthetase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K8D
- Type
- protein
- Length
- 984 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
- Ligands
- CTP, KDO, MG
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 3-deoxy-manno-octulosonate cytidylyltransferase (EC 2.7.7.38) | protein | 246 | 35% helix, 22% strand | P04951 |
Ligands and binding sites
- CTP · Cytidine-5'-triphosphate · ligand · 4 copies · chains A, D, B, C
- KDO · 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid · sugar · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.81 | 0.90 | 47 | MG, KDO, CTP |
| 2 | 430 | 0.80 | 0.89 | 49 | MG, KDO, CTP |
| 3 | 435 | 0.80 | 0.89 | 50 | MG, KDO, CTP |
| 4 | 422 | 0.80 | 0.89 | 46 | MG, KDO, CTP |
| 5 | 119 | 0.64 | 0.88 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1281 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1266 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 282 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 60 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3K8D · Crystal structure of E. coli lipopolysaccharide specific CMP-KDO synthetase in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- P04951 · AlphaFold monomer V2.0 prediction for 3-deoxy-manno-octulosonate cytidylyltransferase… · a predicted model of the same protein · chain A against A, TM-score 0.93
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 3K8D · PDBe 3K8D · UniProt P04951
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.