MolNFT v1 · #164954 · protein
Crystal structure of full-length human lysyl hydroxylase LH3 - cocrystal with FE2+, MN2+, udp-glucuronic acid
6TES · Procollagen-LYSINE,2-oxoglutarate 5-dioxygenase 3: “Crystal structure of full-length human lysyl hydroxylase LH3 - cocrystal with FE2+, MN2+, udp-glucuronic acid”. X-ray diffraction, 5 ligands (AKG, UGA, NAG), 6 pockets (best…
- PDB
- 6TES
- 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, 2.4.1.50, 2.4.1.66
- UniProt
- O60568
- Ligands
- AKG, UGA, NAG, FE2, MN
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Procollagen-LYSINE,2-oxoglutarate 5-dioxygenase 3 (EC 1.14.11.4, 2.4.1.50, 2.4.1.66) | protein | 700 | 31% helix, 27% strand | O60568 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · chains A
- UGA · Uridine-5'-diphosphate-glucuronic acid · 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
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.78 | 0.98 | 30 | AKG, FE2 |
| 2 | 749 | 0.75 | 0.80 | 79 | UGA, EDO |
| 3 | 164 | 0.72 | 0.90 | 31 | EDO |
| 4 | 234 | 0.53 | 0.76 | 34 | empty |
| 5 | 52 | 0.33 | 0.78 | 15 | empty |
Modifications
Observed in the structure: 3 disulfide, 2 glycan, 1 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 6TES · 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 6TES · PDBe 6TES · UniProt O60568
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