MolNFT v1 · #96774 · protein
Crystal structure of F114R/R117Q/F139G mutant of 3-deoxy-D-manno- octulosonate 8-phosphate synthase (KDO8PS) from neisseria meningitidis
4JTI · 2-dehydro-3-deoxyphosphooctonate aldolase: “Crystal structure of F114R/R117Q/F139G mutant of 3-deoxy-D-manno- octulosonate 8-phosphate synthase (KDO8PS)…”. X-ray diffraction, 1 ligand (CL), 9 pockets (best druggability 0.79). MolNFT…
- PDB
- 4JTI
- Type
- protein
- Length
- 1,026 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
- CL
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 253 | 44% helix, 19% strand | Q9JZ55 |
| B | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 257 | 43% helix, 19% strand | Q9JZ55 |
| C, D | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 258 | 43% helix, 21% strand | Q9JZ55 |
Ligands and binding sites
- CL · Chloride ion · ion · 5 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 867 | 0.79 | 0.82 | 92 | CL |
| 2 | 876 | 0.78 | 0.81 | 92 | CL |
| 3 | 327 | 0.65 | 0.80 | 40 | empty |
| 4 | 119 | 0.61 | 0.86 | 27 | empty |
| 5 | 180 | 0.61 | 0.83 | 27 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1533 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 1489 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1417 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1341 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 246 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4JTI · Crystal structure of F114R/R117Q/F139G 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 4JTI · PDBe 4JTI · UniProt Q9JZ55
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