Research workbench
Crystal structure of a putative aldehyde dehydrogenase from burkholderia cenocepacia
Analyse Crystal structure of a putative aldehyde dehydrogenase from burkholderia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YWE
- Type
- protein
- Length
- 3,806 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative aldehyde dehydrogenase
- UniProt
- B4E8B7
- Ligands
- CA, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G | Putative aldehyde dehydrogenase | protein | 476 | 43% helix, 24% strand | B4E8B7 |
| H | Putative aldehyde dehydrogenase | protein | 474 | 42% helix, 23% strand | B4E8B7 |
Ligands and binding sites
- CA · Calcium ion · metal · 11 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, E
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, B, C, D, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 651 | 0.86 | 0.91 | 83 | EDO |
| 2 | 638 | 0.86 | 0.91 | 80 | MG |
| 3 | 489 | 0.85 | 0.92 | 53 | empty |
| 4 | 398 | 0.84 | 0.93 | 47 | EDO |
| 5 | 370 | 0.84 | 0.92 | 41 | empty |
Interfaces
14 interfaces between chains.
- C–D · 2392 Ų buried · 34 hydrogen bonds · protein-protein
- G–H · 2369 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2366 Ų buried · 33 hydrogen bonds · protein-protein
- E–F · 2312 Ų buried · 34 hydrogen bonds · protein-protein
- E–H · 950 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4YWE · 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 B4E8B7
- Elsewhere: RCSB PDB 4YWE · PDBe 4YWE · UniProt B4E8B7
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