Research workbench
Crystal structure of the FE(II)/ALPHA-ketoglutarate dependent dioxygenase KDO1 with FE(II)/SUCCINATE/(3S)-3-hydroxy-L-lysine
Analyse Crystal structure of the FE(II)/ALPHA-ketoglutarate dependent dioxygenase KDO1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F6J
- Type
- protein
- Length
- 1,302 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
- Ligands
- CUW, FE
- Pockets
- 19 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | L-lysine 3-hydroxylase (EC 1.14.11.-) | protein | 325 | 31% helix, 23% strand | C7QJ42 |
| B, D | L-lysine 3-hydroxylase (EC 1.14.11.-) | protein | 326 | 32% helix, 23% strand | C7QJ42 |
Ligands and binding sites
- CUW · (2~{S},3~{R})-2,6-bis(azanyl)-3-oxidanyl-hexanoic acid · ligand · 4 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- SIN · Succinic acid · additive · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 2 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.82 | 0.97 | 40 | empty |
| 2 | 189 | 0.80 | 0.95 | 41 | empty |
| 3 | 150 | 0.76 | 0.94 | 31 | FE, SIN, CUW |
| 4 | 137 | 0.75 | 0.94 | 29 | FE, SIN, CUW |
| 5 | 303 | 0.71 | 0.85 | 49 | FE, SIN, CUW |
Interfaces
4 interfaces between chains.
- C–D · 1489 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1460 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 352 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 330 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6F6J · Crystal structure of the Fe(II)/alpha-ketoglutarate dependent dioxygenase KDO1 with… · the same entry in another collection · chain D against D, TM-score 1.00
- C7QJ42 · AlphaFold monomer V2.0 prediction for L-lysine 3-hydroxylase (C7QJ42) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 6F6J · PDBe 6F6J · UniProt C7QJ42
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