MolNFT v1 · #107761 · protein
Structural analysis of substrate-mimicking inhibitors in complex with neisseria meningitidis 3 deoxy D arabino heptulosonate 7 phosphate synthase the importance of accommodating the active site water
4UMA · Phospho-2-dehydro-3-deoxyheptonate aldolase: “Structural analysis of substrate-mimicking inhibitors in complex with neisseria meningitidis 3 deoxy D…”. X-ray diffraction, 2 ligands (GZ3, MN), 16 pockets (best druggability 0.71).…
- PDB
- 4UMA
- Type
- protein
- Length
- 1,334 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
- GZ3, MN
- Pockets
- 16 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 333 | 42% helix, 18% strand | Q9K169 |
| C, D | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 334 | 41% helix, 17% strand | Q9K169 |
Ligands and binding sites
- GZ3 · (E)-2-methyl-3-phosphonoacrylate · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.71 | 0.98 | 16 | empty |
| 2 | 53 | 0.70 | 0.98 | 17 | empty |
| 3 | 54 | 0.70 | 0.98 | 17 | empty |
| 4 | 242 | 0.67 | 0.84 | 47 | empty |
| 5 | 82 | 0.63 | 0.91 | 22 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2098 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2026 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 587 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 534 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 75 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4UMA · Structural analysis of substrate-mimicking inhibitors in complex with Neisseria… · 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 4UMA · PDBe 4UMA · UniProt Q9K169
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