MolNFT v1 · #71526 · protein
Structure of S. cerevisiae TPA1 protein, a proline hydroxylase modifying ribosomal protein RPS23
3MGU · Pkhd-type hydroxylase TPA1: “Structure of S. cerevisiae TPA1 protein, a proline hydroxylase modifying ribosomal protein RPS23”. X-ray diffraction, 1 ligand (FE2), 6 pockets (best druggability 0.74). MolNFT v1 #71526 on GenesisL1: 3D…
- PDB
- 3MGU
- Type
- protein
- Length
- 533 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pkhd-type hydroxylase TPA1
- EC
- 1.14.11.-
- UniProt
- P40032
- Ligands
- FE2
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pkhd-type hydroxylase TPA1 (EC 1.14.11.-) | protein | 533 | 30% helix, 27% strand | P40032 |
Ligands and binding sites
- FE2 · Fe (II) ion · metal · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.74 | 0.88 | 29 | empty |
| 2 | 53 | 0.67 | 0.96 | 19 | FE2 |
| 3 | 110 | 0.58 | 0.85 | 31 | empty |
| 4 | 102 | 0.48 | 0.81 | 20 | empty |
| 5 | 86 | 0.37 | 0.76 | 13 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3MGU · Structure of S. cerevisiae Tpa1 protein, a proline hydroxylase modifying ribosomal… · the same entry in another collection · chain A against A, TM-score 1.00
- P40032 · AlphaFold monomer V2.0 prediction for prolyl 3,4-dihydroxylase TPA1 (P40032) · a predicted model of the same protein · chain A 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 P40032
- Elsewhere: RCSB PDB 3MGU · PDBe 3MGU · UniProt P40032
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