MolNFT v1 · #115991 · protein
Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphate synthase GLU176GLN variant
5D02 · Phospho-2-dehydro-3-deoxyheptonate aldolase: “Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphate synthase GLU176GLN variant”. X-ray diffraction, 3 ligands (PEP, MN, SO4), 15 pockets (best druggability 0.77). MolNFT…
- PDB
- 5D02
- Type
- protein
- Length
- 1,336 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospho-2-dehydro-3-deoxyheptonate aldolase
- EC
- 2.5.1.54
- UniProt
- Q9K169
- Ligands
- PEP, MN, SO4
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 334 | 42% helix, 16% strand | Q9K169 |
| B | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 335 | 41% helix, 17% strand | Q9K169 |
| C | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 333 | 42% helix, 18% strand | Q9K169 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 472 | 0.77 | 0.85 | 79 | PEP |
| 2 | 52 | 0.71 | 0.98 | 16 | empty |
| 3 | 50 | 0.70 | 0.98 | 16 | empty |
| 4 | 53 | 0.70 | 0.98 | 17 | empty |
| 5 | 279 | 0.66 | 0.82 | 48 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2194 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1949 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 577 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 558 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 64 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5D02 · Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphate synthase Glu176Gln… · 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 Q9K169
- Elsewhere: RCSB PDB 5D02 · PDBe 5D02 · UniProt Q9K169
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