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Crystal structure of full-length human lysyl hydroxylase LH3 - cocrystal with FE2+, MN2+, udp-gal
Analyse Crystal structure of full-length human lysyl hydroxylase LH3 - cocrystal with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FXR
- Type
- protein
- Length
- 700 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Procollagen-LYSINE,2-oxoglutarate 5-dioxygenase 3
- EC
- 1.14.11.4
- UniProt
- O60568
- Ligands
- AKG, UDP, NAG, FE2, MN
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Procollagen-LYSINE,2-oxoglutarate 5-dioxygenase 3 (EC 1.14.11.4) | protein | 700 | 30% helix, 27% strand | O60568 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · chains A
- UDP · Uridine-5'-diphosphate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- FE2 · Fe (II) ion · metal · 2 copies · chains A
- MN · Manganese (II) ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 709 | 0.74 | 0.79 | 75 | GOL, UDP |
| 2 | 52 | 0.72 | 0.99 | 20 | AKG, FE2 |
| 3 | 166 | 0.71 | 0.89 | 27 | empty |
| 4 | 159 | 0.43 | 0.74 | 25 | empty |
| 5 | 60 | 0.31 | 0.76 | 18 | empty |
Modifications
Observed in the structure: 3 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6FXR · Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Cocrystal with Fe2+, Mn2+… · the same entry in another collection · chain A against A, TM-score 1.00
- O60568 · AlphaFold monomer V2.0 prediction for multifunctional procollagen lysine hydroxylase and… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O60568
- Elsewhere: RCSB PDB 6FXR · PDBe 6FXR · UniProt O60568
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