Research workbench
Crystal structure of the complex FE(II)/ALPHA-ketoglutarate dependent dioxygenase KDO1 with FE(II)/LYSINE
Analyse Crystal structure of the complex FE(II)/ALPHA-ketoglutarate dependent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F2A
- Type
- protein
- Length
- 1,299 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
- LYS, FE2, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 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 | 324 | 30% helix, 23% strand | C7QJ42 |
| C | L-lysine 3-hydroxylase (EC 1.14.11.-) | protein | 326 | 30% helix, 23% strand | C7QJ42 |
Ligands and binding sites
- LYS · Lysine · ligand · 5 copies · chains A, B, C, D
- FE2 · Fe (II) ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains A
- ACY · Acetic acid · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.81 | 0.96 | 40 | empty |
| 2 | 190 | 0.80 | 0.95 | 40 | empty |
| 3 | 139 | 0.76 | 0.94 | 29 | FE2, LYS |
| 4 | 145 | 0.75 | 0.93 | 32 | FE2, LYS |
| 5 | 133 | 0.75 | 0.94 | 29 | FE2, LYS |
Interfaces
4 interfaces between chains.
- C–D · 1489 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1459 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 324 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 323 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6F2A · Crystal structure of the complex Fe(II)/alpha-ketoglutarate dependent dioxygenase KDO1… · 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 D 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 6F2A · PDBe 6F2A · UniProt C7QJ42
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