MolNFT v1 · #179005 · protein
Hydroxylase homolog of besd with FE(II), alpha-ketoglutarate, and lysine
7JSD · Lysine hydroxylase: “Hydroxylase homolog of besd with FE(II), alpha-ketoglutarate, and lysine”. X-ray diffraction, 3 ligands (AKG, LYS, FE2), 14 pockets (best druggability 0.81). MolNFT v1 #179005 on GenesisL1: 3D structure, binding…
- PDB
- 7JSD
- Type
- protein
- Length
- 989 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine hydroxylase
- Ligands
- AKG, LYS, FE2
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine hydroxylase | protein | 254 | 33% helix, 28% strand | — |
| B | Lysine hydroxylase | protein | 256 | 33% helix, 26% strand | — |
| C | Lysine hydroxylase | protein | 256 | 34% helix, 26% strand | — |
| D | Lysine hydroxylase | protein | 223 | 42% helix, 24% strand | — |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 4 copies · chains A, B, C, D
- LYS · Lysine · ligand · 3 copies · chains A, B, C
- FE2 · Fe (II) ion · metal · 4 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.81 | 0.99 | 31 | LYS, AKG, FE2 |
| 2 | 125 | 0.79 | 0.97 | 31 | LYS, AKG, FE2 |
| 3 | 117 | 0.79 | 0.98 | 31 | LYS, AKG |
| 4 | 653 | 0.72 | 0.79 | 65 | PG4 |
| 5 | 499 | 0.71 | 0.81 | 57 | empty |
Interfaces
4 interfaces between chains.
- A–B · 699 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 696 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 640 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 625 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 7JSD · Hydroxylase homolog of BesD with Fe(II), alpha-ketoglutarate, and lysine · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 7JSD · PDBe 7JSD
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