MolNFT v1 · #148021 · protein
Crystal structure of apo FE(II)/ALPHA-ketoglutarate dependent dioxygenase KDO5
6EUO · L-lysine 4-hydroxylase: “Crystal structure of apo FE(II)/ALPHA-ketoglutarate dependent dioxygenase KDO5”. X-ray diffraction, 3 ligands (MLT, FE, SO4), 20 pockets (best druggability 0.72). MolNFT v1 #148021 on GenesisL1: 3D…
- PDB
- 6EUO
- Type
- protein
- Length
- 1,379 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
- MLT, FE, SO4
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lysine 4-hydroxylase (EC 1.14.11.-) | protein | 346 | 30% helix, 25% strand | J3BZS6 |
| B | L-lysine 4-hydroxylase (EC 1.14.11.-) | protein | 335 | 30% helix, 23% strand | J3BZS6 |
| C | L-lysine 4-hydroxylase (EC 1.14.11.-) | protein | 354 | 30% helix, 24% strand | J3BZS6 |
| D | L-lysine 4-hydroxylase (EC 1.14.11.-) | protein | 344 | 28% helix, 24% strand | J3BZS6 |
Ligands and binding sites
- MLT · D-malate · ligand · 4 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, C, D
- GOL · Glycerol · additive · 7 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.72 | 0.84 | 42 | FE, MLT, SO4 |
| 2 | 330 | 0.68 | 0.82 | 41 | FE, MLT, SO4 |
| 3 | 328 | 0.68 | 0.82 | 40 | FE, MLT, SO4 |
| 4 | 229 | 0.66 | 0.84 | 33 | FE, MLT |
| 5 | 416 | 0.61 | 0.76 | 48 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1542 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1527 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 644 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 460 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 402 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6EUO · Crystal structure of APO 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 6EUO · PDBe 6EUO · UniProt J3BZS6
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