MolNFT v1 · #96773 · protein
Crystal structure of F114R/R117Q mutant of 3-deoxy-D-manno- octulosonate 8-phosphate synthase (KDO8PS) from neisseria meningitidis
4JTH · 2-dehydro-3-deoxyphosphooctonate aldolase: “Crystal structure of F114R/R117Q mutant of 3-deoxy-D-manno- octulosonate 8-phosphate synthase (KDO8PS) from…”. X-ray diffraction, 2 ligands (NA, CL), 13 pockets (best druggability 0.72).…
- PDB
- 4JTH
- Type
- protein
- Length
- 1,016 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-dehydro-3-deoxyphosphooctonate aldolase
- EC
- 2.5.1.55
- UniProt
- Q9JZ55
- Ligands
- NA, CL
- Pockets
- 13 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 250 | 44% helix, 20% strand | Q9JZ55 |
| B | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 251 | 42% helix, 20% strand | Q9JZ55 |
| C | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 259 | 44% helix, 21% strand | Q9JZ55 |
| D | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 256 | 44% helix, 21% strand | Q9JZ55 |
Ligands and binding sites
- NA · Sodium ion · metal · chains C
- CL · Chloride ion · ion · 5 copies · chains B, C, D
- GOL · Glycerol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 386 | 0.72 | 0.83 | 46 | CL |
| 2 | 364 | 0.67 | 0.81 | 44 | CL |
| 3 | 372 | 0.67 | 0.81 | 46 | empty |
| 4 | 354 | 0.66 | 0.80 | 40 | empty |
| 5 | 199 | 0.59 | 0.81 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1544 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 1501 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1366 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1339 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 219 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4JTH · Crystal structure of F114R/R117Q mutant of 3-deoxy-D-manno-octulosonate 8-phosphate… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9JZ55
- Elsewhere: RCSB PDB 4JTH · PDBe 4JTH · UniProt Q9JZ55
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.