MolNFT v1 · #115982 · protein
Neisseria meningitidis 3 dexy-D-arabino-heptulosonate 7-phosphate synthase GLU176ALA variant
5CZT · Phospho-2-dehydro-3-deoxyheptonate aldolase: “Neisseria meningitidis 3 dexy-D-arabino-heptulosonate 7-phosphate synthase GLU176ALA variant”. X-ray diffraction, 3 ligands (PHE, MN, CL), 10 pockets (best druggability 0.79). MolNFT v1…
- PDB
- 5CZT
- Type
- protein
- Length
- 1,382 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
- PHE, MN, CL
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 346 | 41% helix, 19% strand | Q9K169 |
| B | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 344 | 41% helix, 19% strand | Q9K169 |
Ligands and binding sites
- PHE · Phenylalanine · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 3 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 517 | 0.79 | 0.86 | 87 | CL |
| 2 | 519 | 0.76 | 0.84 | 66 | empty |
| 3 | 368 | 0.75 | 0.86 | 66 | empty |
| 4 | 468 | 0.75 | 0.84 | 73 | CL |
| 5 | 65 | 0.71 | 0.97 | 19 | PHE |
Interfaces
6 interfaces between chains.
- A–B · 3191 Ų buried · 58 hydrogen bonds · protein-protein
- C–D · 3177 Ų buried · 56 hydrogen bonds · protein-protein
- A–C · 521 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 517 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 111 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5CZT · Neisseria meningitidis 3 dexy-D-arabino-heptulosonate 7-phosphate synthase Glu176Ala… · 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 5CZT · PDBe 5CZT · UniProt Q9K169
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