MolNFT v1 · #144198 · protein
The structure of a dimeric type II DAH7PS associated with pyocyanin biosynthesis in pseudomonas aeruginosa
6BMC · Phospho-2-dehydro-3-deoxyheptonate aldolase: “The structure of a dimeric type II DAH7PS associated with pyocyanin biosynthesis in pseudomonas aeruginosa”. X-ray diffraction, 3 ligands (PEP, CO, CL), 7 pockets (best druggability…
- PDB
- 6BMC
- Type
- protein
- Length
- 760 residues
- Chains
- 2
- 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
- G3XCJ9
- Ligands
- PEP, CO, CL
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 380 | 39% helix, 15% strand | G3XCJ9 |
| B | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 380 | 39% helix, 15% strand | G3XCJ9 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · 2 copies · chains A, B
- CO · Cobalt (II) ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 547 | 0.63 | 0.75 | 48 | empty |
| 2 | 113 | 0.53 | 0.83 | 19 | PEP |
| 3 | 137 | 0.49 | 0.79 | 23 | PEP |
| 4 | 58 | 0.30 | 0.75 | 13 | empty |
| 5 | 64 | 0.29 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 872 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6BMC · The structure of a dimeric type II DAH7PS associated with pyocyanin biosynthesis in… · 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 G3XCJ9
- Elsewhere: RCSB PDB 6BMC · PDBe 6BMC · UniProt G3XCJ9
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