MolNFT v1 · #148117 · protein
Crystal structure of the complex FE(II)/ALPHA-ketoglutarate dependent dioxygenase KDO5 with FE(II)/LYSINE
6EXF · L-lysine 4-hydroxylase: “Crystal structure of the complex FE(II)/ALPHA-ketoglutarate dependent dioxygenase KDO5 with FE(II)/LYSINE”. X-ray diffraction, 2 ligands (LYS, FE), 18 pockets (best druggability 0.75). MolNFT v1 #148117 on…
- PDB
- 6EXF
- Type
- protein
- Length
- 1,356 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lysine 4-hydroxylase
- EC
- 1.14.11.-
- UniProt
- J3BZS6
- Ligands
- LYS, FE
- Pockets
- 18 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lysine 4-hydroxylase (EC 1.14.11.-) | protein | 343 | 30% helix, 24% strand | J3BZS6 |
| B | L-lysine 4-hydroxylase (EC 1.14.11.-) | protein | 315 | 30% helix, 23% strand | J3BZS6 |
| C | L-lysine 4-hydroxylase (EC 1.14.11.-) | protein | 352 | 27% helix, 24% strand | J3BZS6 |
| D | L-lysine 4-hydroxylase (EC 1.14.11.-) | protein | 346 | 29% helix, 24% strand | J3BZS6 |
Ligands and binding sites
- LYS · Lysine · ligand · 5 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 205 | 0.75 | 0.90 | 45 | FE, LYS |
| 2 | 291 | 0.75 | 0.88 | 41 | FE, LYS |
| 3 | 213 | 0.68 | 0.85 | 37 | FE, LYS |
| 4 | 245 | 0.63 | 0.82 | 46 | FE, LYS |
| 5 | 239 | 0.60 | 0.80 | 36 | GOL |
Interfaces
5 interfaces between chains.
- C–D · 1551 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1528 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 637 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 447 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 405 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6EXF · Crystal structure of the complex Fe(II)/alpha-ketoglutarate dependent dioxygenase KDO5… · the same entry in another collection · chain D against D, TM-score 1.00
- J3BZS6 · AlphaFold monomer V2.0 prediction for L-lysine 4-hydroxylase (J3BZS6) · a predicted model of the same protein · chain A 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 J3BZS6
- Elsewhere: RCSB PDB 6EXF · PDBe 6EXF · UniProt J3BZS6
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