MolNFT v1 · #96776 · protein
Crystal structure of R117Q mutant of 3-deoxy-D-manno-octulosonate 8- phosphate synthase (KDO8PS) from neisseria meningitidis
4JTK · 2-dehydro-3-deoxyphosphooctonate aldolase: “Crystal structure of R117Q mutant of 3-deoxy-D-manno-octulosonate 8- phosphate synthase (KDO8PS) from…”. X-ray diffraction, 2 ligands (NA, CL), 10 pockets (best druggability 0.69). MolNFT…
- PDB
- 4JTK
- Type
- protein
- Length
- 1,018 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
- 10 · best druggability 0.69
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 | 252 | 42% helix, 20% strand | Q9JZ55 |
| B | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 253 | 43% helix, 19% strand | Q9JZ55 |
| C | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 256 | 43% helix, 21% strand | Q9JZ55 |
| D | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 257 | 42% helix, 21% strand | Q9JZ55 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 473 | 0.69 | 0.80 | 51 | CL |
| 2 | 407 | 0.68 | 0.81 | 47 | CL |
| 3 | 408 | 0.68 | 0.80 | 38 | empty |
| 4 | 358 | 0.67 | 0.81 | 45 | CL |
| 5 | 355 | 0.66 | 0.80 | 43 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1530 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1448 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1388 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1274 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 236 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4JTK · Crystal structure of R117Q mutant of 3-deoxy-D-manno-octulosonate 8-phosphate synthase… · 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 4JTK · PDBe 4JTK · UniProt Q9JZ55
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