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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
Analyse Structural analysis of substrate-mimicking inhibitors in complex with neisseria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UMC
- 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
- PEQ, MN, PO4
- Pockets
- 11 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 334 | 42% helix, 17% strand | Q9K169 |
| B | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 334 | 40% helix, 17% strand | Q9K169 |
| C | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 335 | 41% helix, 18% strand | Q9K169 |
| D | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 333 | 42% helix, 17% strand | Q9K169 |
Ligands and binding sites
- PEQ · L-phospholactate · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.64 | 0.91 | 24 | empty |
| 2 | 89 | 0.60 | 0.89 | 25 | empty |
| 3 | 190 | 0.60 | 0.82 | 38 | empty |
| 4 | 240 | 0.59 | 0.79 | 43 | empty |
| 5 | 196 | 0.56 | 0.80 | 40 | PO4, PEQ |
Interfaces
6 interfaces between chains.
- C–D · 2107 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2089 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 602 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 566 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 78 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4UMC · 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 4UMC · PDBe 4UMC · UniProt Q9K169
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