MolNFT v1 · #49318 · protein
Crystal structure of 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8PS) from neisseria meningitidis
2QKF · 3-deoxy-D-manno-octulosonic acid 8- phosphate synthetase: “Crystal structure of 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8PS) from neisseria meningitidis”. X-ray diffraction, 2 ligands (NA, CL), 12 pockets (best…
- PDB
- 2QKF
- Type
- protein
- Length
- 1,011 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-deoxy-D-manno-octulosonic acid 8- phosphate synthetase
- EC
- 2.5.1.55
- UniProt
- Q9JZ55
- Ligands
- NA, CL
- Pockets
- 12 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-deoxy-D-manno-octulosonic acid 8- phosphate synthetase (EC 2.5.1.55) | protein | 251 | 44% helix, 21% strand | Q9JZ55 |
| B | 3-deoxy-D-manno-octulosonic acid 8- phosphate synthetase (EC 2.5.1.55) | protein | 251 | 42% helix, 21% strand | Q9JZ55 |
| C | 3-deoxy-D-manno-octulosonic acid 8- phosphate synthetase (EC 2.5.1.55) | protein | 256 | 43% helix, 22% strand | Q9JZ55 |
| D | 3-deoxy-D-manno-octulosonic acid 8- phosphate synthetase (EC 2.5.1.55) | protein | 253 | 43% helix, 21% strand | Q9JZ55 |
Ligands and binding sites
- NA · Sodium ion · metal · chains C
- CL · Chloride ion · ion · 5 copies · chains B, D, C
- GOL · Glycerol · additive · 4 copies · chains C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.69 | 0.81 | 44 | CL |
| 2 | 383 | 0.68 | 0.81 | 39 | empty |
| 3 | 385 | 0.68 | 0.81 | 41 | empty |
| 4 | 378 | 0.68 | 0.81 | 43 | CL |
| 5 | 166 | 0.62 | 0.84 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1557 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 1514 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1339 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 1331 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 205 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2QKF · Crystal structure of 3-deoxy-d-manno-octulosonate 8-phosphate synthase (KDO8PS) from… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9JZ55 · AlphaFold monomer V2.0 prediction for 2-dehydro-3-deoxyphosphooctonate aldolase (Q9JZ55) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 2QKF · PDBe 2QKF · UniProt Q9JZ55
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