Research workbench
Crystal structure of the apo FE(II)/ALPHA-ketoglutarate dependent dioxygenase KDO1
Analyse Crystal structure of the apo FE(II)/ALPHA-ketoglutarate dependent dioxygenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F2E
- Type
- protein
- Length
- 1,308 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lysine 3-hydroxylase
- EC
- 1.14.11.-
- UniProt
- C7QJ42
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L-lysine 3-hydroxylase (EC 1.14.11.-) | protein | 329 | 32% helix, 24% strand | C7QJ42 |
| C | L-lysine 3-hydroxylase (EC 1.14.11.-) | protein | 328 | 33% helix, 23% strand | C7QJ42 |
| D | L-lysine 3-hydroxylase (EC 1.14.11.-) | protein | 322 | 32% helix, 24% strand | C7QJ42 |
Ligands and binding sites
- ACY · Acetic acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 179 | 0.82 | 0.97 | 39 | empty |
| 2 | 180 | 0.80 | 0.95 | 36 | empty |
| 3 | 316 | 0.71 | 0.84 | 51 | ACY |
| 4 | 245 | 0.70 | 0.86 | 44 | ACY |
| 5 | 554 | 0.69 | 0.79 | 68 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1513 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1510 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 358 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 346 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6F2E · Crystal structure of the APO Fe(II)/alpha-ketoglutarate dependent dioxygenase KDO1 · the same entry in another collection · chain A against A, TM-score 1.00
- C7QJ42 · AlphaFold monomer V2.0 prediction for L-lysine 3-hydroxylase (C7QJ42) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 C7QJ42
- Elsewhere: RCSB PDB 6F2E · PDBe 6F2E · UniProt C7QJ42
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