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Crystal structure of a novel N-substituted L-amino acid dioxygenase in complex with alpha-kg from burkholderia ambifaria ammd
Analyse Crystal structure of a novel N-substituted L-amino acid dioxygenase in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3W21
- Type
- protein
- Length
- 503 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein
- UniProt
- Q0B2N4
- Ligands
- AKG, ZN
- Pockets
- 7 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uncharacterized protein | protein | 253 | 28% helix, 28% strand | Q0B2N4 |
| B | Putative uncharacterized protein | protein | 250 | 28% helix, 28% strand | Q0B2N4 |
Ligands and binding sites
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 | 307 | 0.62 | 0.79 | 45 | AKG |
| 2 | 206 | 0.56 | 0.79 | 34 | ZN |
| 3 | 109 | 0.38 | 0.74 | 19 | empty |
| 4 | 91 | 0.36 | 0.75 | 17 | empty |
| 5 | 58 | 0.35 | 0.78 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1191 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified, 1 disulfide (engineered, disulfide).
Compared structures
- 3W21 · Crystal Structure of a Novel N-Substituted L-Amino Acid Dioxygenase in complex with… · 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 Q0B2N4
- Elsewhere: RCSB PDB 3W21 · PDBe 3W21 · UniProt Q0B2N4
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