MolNFT v1 · #144234 · protein
Structure of 2-dehydro-3-deoxyphosphooctonate aldolase from acinetobacter baumannii
6BNG: “Structure of 2-dehydro-3-deoxyphosphooctonate aldolase from acinetobacter baumannii”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.68). MolNFT v1 #144234 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6BNG
- Type
- protein
- Length
- 547 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-dehydro-3-deoxyphosphooctonate aldolase
- EC
- 2.5.1.55
- UniProt
- B7H226
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 277 | 42% helix, 20% strand | B7H226 |
| B | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 270 | 42% helix, 20% strand | B7H226 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 252 | 0.68 | 0.84 | 32 | SO4 |
| 2 | 202 | 0.60 | 0.82 | 34 | SO4 |
| 3 | 77 | 0.59 | 0.88 | 26 | empty |
| 4 | 306 | 0.53 | 0.75 | 49 | empty |
| 5 | 183 | 0.47 | 0.76 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1798 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6BNG · Structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Acinetobacter baumannii · the same entry in another collection · chain A against A, TM-score 1.00
- B7H226 · AlphaFold monomer V2.0 prediction for 2-dehydro-3-deoxyphosphooctonate aldolase (B7H226) · a predicted model of the same protein · chain B 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 B7H226
- Elsewhere: RCSB PDB 6BNG · PDBe 6BNG · UniProt B7H226
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