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Crystal structure of the complex FE(II)/ALPHA-ketoglutarate dependent dioxygenase KDO5 with FE(II)/SUCCINATE/(4R)-4-hydroxy-L-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
- 6EXH
- Type
- protein
- Length
- 1,387 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
- LYO, FE
- Pockets
- 16 · best druggability 0.74
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 | 348 | 30% helix, 25% strand | J3BZS6 |
| B | L-lysine 4-hydroxylase (EC 1.14.11.-) | protein | 336 | 30% helix, 23% strand | J3BZS6 |
| C | L-lysine 4-hydroxylase (EC 1.14.11.-) | protein | 353 | 29% helix, 24% strand | J3BZS6 |
| D | L-lysine 4-hydroxylase (EC 1.14.11.-) | protein | 350 | 29% helix, 23% strand | J3BZS6 |
Ligands and binding sites
- LYO · 4-hydroxy-lysine · ligand · 4 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- SIN · Succinic acid · additive · 3 copies · chains A, B, D
- GOL · Glycerol · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.74 | 0.91 | 41 | LYO |
| 2 | 203 | 0.73 | 0.89 | 48 | FE, SIN, LYO |
| 3 | 305 | 0.67 | 0.82 | 42 | FE, LYO, SIN |
| 4 | 197 | 0.66 | 0.85 | 38 | LYO, SIN |
| 5 | 226 | 0.61 | 0.81 | 25 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1527 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1514 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 666 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 469 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 402 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6EXH · 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 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 J3BZS6
- Elsewhere: RCSB PDB 6EXH · PDBe 6EXH · UniProt J3BZS6
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