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Crystal structure of the triple mutant (N23C/D247E/P249A) of 3-deoxy- D-manno-octulosonate 8-phosphate synthase (KDO8PS) from neisseria meningitidis
Analyse Crystal structure of the triple mutant (N23C/D247E/P249A) of 3-deoxy… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FYO
- Type
- protein
- Length
- 1,034 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
- PEP, NA, MN, CL
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 42% 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 | 255 | 43% helix, 20% strand | Q9JZ55 |
| B | 3-deoxy-D-manno-octulosonic acid 8-phosphate synthetase (EC 2.5.1.55) | protein | 262 | 41% helix, 20% strand | Q9JZ55 |
| C | 3-deoxy-D-manno-octulosonic acid 8-phosphate synthetase (EC 2.5.1.55) | protein | 256 | 41% helix, 21% strand | Q9JZ55 |
| D | 3-deoxy-D-manno-octulosonic acid 8-phosphate synthetase (EC 2.5.1.55) | protein | 261 | 42% helix, 21% strand | Q9JZ55 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · chains D
- NA · Sodium ion · metal · chains C
- MN · Manganese (II) ion · metal · chains D
- CL · Chloride ion · ion · 2 copies · chains B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 555 | 0.77 | 0.84 | 53 | empty |
| 2 | 477 | 0.75 | 0.84 | 45 | PEP, MN |
| 3 | 362 | 0.69 | 0.82 | 36 | CL |
| 4 | 392 | 0.66 | 0.79 | 33 | empty |
| 5 | 228 | 0.60 | 0.81 | 26 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1545 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 1485 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1461 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1237 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 206 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3FYO · Crystal structure of the triple mutant (N23C/D247E/P249A) of 3-deoxy-D-manno-octulosonate… · 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 3FYO · PDBe 3FYO · UniProt Q9JZ55
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