MolNFT v1 · #101939 · protein
Crystal structure of a putative aldehyde dehydrogenase from burkholderia cenocepacia
4O6R: “Crystal structure of a putative aldehyde dehydrogenase from burkholderia cenocepacia”. X-ray diffraction, 2 ligands (AMP, NO3), 13 pockets (best druggability 0.86). MolNFT v1 #101939 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4O6R
- Type
- protein
- Length
- 1,956 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldehyde dehydrogenase
- UniProt
- B4EJX1
- Ligands
- AMP, NO3
- Pockets
- 13 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Aldehyde dehydrogenase | protein | 489 | 42% helix, 21% strand | B4EJX1 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
- NO3 · Nitrate ion · ion · 8 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 872 | 0.86 | 0.88 | 111 | EDO |
| 2 | 1040 | 0.86 | 0.87 | 122 | empty |
| 3 | 1156 | 0.85 | 0.86 | 48 | empty |
| 4 | 469 | 0.79 | 0.87 | 51 | EDO |
| 5 | 424 | 0.79 | 0.87 | 39 | EDO |
Interfaces
6 interfaces between chains.
- A–C · 3128 Ų buried · 47 hydrogen bonds · protein-protein
- B–D · 3110 Ų buried · 48 hydrogen bonds · protein-protein
- C–D · 1025 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1024 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 983 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4O6R · Crystal Structure of a Putative Aldehyde Dehydrogenase from Burkholderia cenocepacia · 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 B4EJX1
- Elsewhere: RCSB PDB 4O6R · PDBe 4O6R · UniProt B4EJX1
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