MolNFT v1 · #165256 · protein
Crystal structure of human transmembrane prolyl 4-hydroxylase
6TP5: “Crystal structure of human transmembrane prolyl 4-hydroxylase”. X-ray diffraction, 8 ligands (OGA, GLY, MAN), 10 pockets (best druggability 0.78). MolNFT v1 #165256 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6TP5
- Type
- protein
- Length
- 726 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transmembrane prolyl 4-hydroxylase
- EC
- 1.14.11.29
- UniProt
- Q9NXG6
- Ligands
- OGA, GLY, MAN, NAG, BMA, CA, FE2, CL
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transmembrane prolyl 4-hydroxylase (EC 1.14.11.29) | protein | 370 | 28% helix, 24% strand | Q9NXG6 |
| B | Transmembrane prolyl 4-hydroxylase (EC 1.14.11.29) | protein | 356 | 29% helix, 25% strand | Q9NXG6 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 2 copies · chains A, B
- GLY · Glycine · ligand · 2 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 13 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 3 copies
- CA · Calcium ion · metal · 4 copies · chains A, B
- FE2 · Fe (II) ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- TBU · Tertiary-butyl alcohol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.78 | 0.90 | 40 | TBU |
| 2 | 104 | 0.75 | 0.96 | 26 | TBU |
| 3 | 232 | 0.67 | 0.83 | 27 | TBU |
| 4 | 353 | 0.62 | 0.78 | 47 | OGA, FE2, TBU |
| 5 | 367 | 0.62 | 0.78 | 48 | OGA, FE2, TBU |
Interfaces
1 interface between chains.
- A–B · 1523 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6TP5 · Crystal structure of human Transmembrane prolyl 4-hydroxylase · the same entry in another collection · chain B against B, TM-score 1.00
- Q9NXG6 · AlphaFold monomer V2.0 prediction for transmembrane prolyl 4-hydroxylase (Q9NXG6) · a predicted model of the same protein · chain B 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
- Every structure of UniProt Q9NXG6
- Elsewhere: RCSB PDB 6TP5 · PDBe 6TP5 · UniProt Q9NXG6
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