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Crystal structure of the E. COLI adaptive response protein aidb in the space group P3(2)
Analyse Crystal structure of the E. COLI adaptive response protein aidb in the space… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U33
- Type
- protein
- Length
- 6,471 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative acyl-CoA dehydrogenase aidb
- EC
- 1.3.99.-
- UniProt
- P33224
- Ligands
- FAD, CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, J, K | Putative acyl-CoA dehydrogenase aidb (EC 1.3.99.-) | protein | 540 | 56% helix, 14% strand | P33224 |
| B, C, D, E, F, G, H, I, L | Putative acyl-CoA dehydrogenase aidb (EC 1.3.99.-) | protein | 539 | 55% helix, 14% strand | P33224 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- CL · Chloride ion · ion · 12 copies · chains A, D, B, C, E, H, F, G, I, L, J, K
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 | 865 | 0.85 | 0.87 | 89 | FAD |
| 2 | 892 | 0.85 | 0.87 | 93 | FAD |
| 3 | 531 | 0.84 | 0.90 | 74 | FAD |
| 4 | 649 | 0.84 | 0.89 | 99 | FAD |
| 5 | 576 | 0.84 | 0.89 | 73 | FAD |
Interfaces
27 interfaces between chains.
- G–H · 3599 Ų buried · 52 hydrogen bonds · protein-protein
- I–J · 3558 Ų buried · 50 hydrogen bonds · protein-protein
- C–D · 3509 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 3494 Ų buried · 48 hydrogen bonds · protein-protein
- E–F · 3448 Ų buried · 49 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 3U33 · Crystal Structure of the E. coli adaptive response protein AidB in the space group P3(2) · the same entry in another collection · chain L against L, 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 P33224
- Elsewhere: RCSB PDB 3U33 · PDBe 3U33 · UniProt P33224
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