Research workbench
Crystal structure of the N59A mutant of the 3-deoxy-D-manno- octulosonate 8-phosphate synthase (KDO8PS) from neisseria meningitidis
Analyse Crystal structure of the N59A mutant of the 3-deoxy-D-manno- octulosonate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QPZ
- Type
- protein
- Length
- 1,009 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, PO4
- Pockets
- 14 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 251 | 45% helix, 20% strand | Q9JZ55 |
| B | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 252 | 43% helix, 19% strand | Q9JZ55 |
| C | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 252 | 44% helix, 21% strand | Q9JZ55 |
| D | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 254 | 43% helix, 21% strand | Q9JZ55 |
Ligands and binding sites
- NA · Sodium ion · metal · chains C
- CL · Chloride ion · ion · 8 copies · chains A, B, D, C
- PO4 · Phosphate ion · ion · chains B
- GOL · Glycerol · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 435 | 0.70 | 0.81 | 47 | CL |
| 2 | 382 | 0.69 | 0.82 | 45 | CL |
| 3 | 393 | 0.68 | 0.81 | 45 | CL |
| 4 | 422 | 0.67 | 0.79 | 51 | CL |
| 5 | 98 | 0.61 | 0.88 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1501 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 1492 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1320 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 1234 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 209 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3QPZ · Crystal structure of the N59A mutant of the 3-deoxy-d-manno-octulosonate 8-phosphate… · 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 3QPZ · PDBe 3QPZ · UniProt Q9JZ55
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