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Crystal structure of a putative alpha-ketoglutarate dependent 2,4-D dioxygenase from burkholderia xenovorans
Analyse Crystal structure of a putative alpha-ketoglutarate dependent 2,4-D dioxygenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J92
- Type
- protein
- Length
- 1,032 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative alpha kg dependent 2,4-D dioxygenase
- EC
- 1.14.11.-
- UniProt
- Q13Q05
- Ligands
- FE2
- Pockets
- 18 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative alpha kg dependent 2,4-D dioxygenase (EC 1.14.11.-) | protein | 258 | 29% helix, 28% strand | Q13Q05 |
| B | Putative alpha kg dependent 2,4-D dioxygenase (EC 1.14.11.-) | protein | 259 | 30% helix, 28% strand | Q13Q05 |
| C | Putative alpha kg dependent 2,4-D dioxygenase (EC 1.14.11.-) | protein | 258 | 28% helix, 28% strand | Q13Q05 |
| D | Putative alpha kg dependent 2,4-D dioxygenase (EC 1.14.11.-) | protein | 257 | 29% helix, 28% strand | Q13Q05 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 660 | 0.82 | 0.86 | 56 | empty |
| 2 | 791 | 0.82 | 0.85 | 39 | empty |
| 3 | 360 | 0.64 | 0.79 | 43 | empty |
| 4 | 407 | 0.62 | 0.77 | 40 | empty |
| 5 | 138 | 0.61 | 0.85 | 29 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1075 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1056 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 342 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 316 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 267 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5J92 · Crystal structure of a putative alpha-ketoglutarate dependent 2,4-D dioxygenase from… · 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 Q13Q05
- Elsewhere: RCSB PDB 5J92 · PDBe 5J92 · UniProt Q13Q05
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