MolNFT v1 · #101122 · protein
Crystal structure of TPA1P from saccharomyces cerevisiae, termination and polyadenylation protein 1, in complex with N-oxalylglycine (nog)
4NHL · Pkhd-type hydroxylase TPA1: “Crystal structure of TPA1P from saccharomyces cerevisiae, termination and polyadenylation protein 1, in…”. X-ray diffraction, 2 ligands (OGA, MN), 5 pockets (best druggability 0.69). MolNFT v1 #101122 on…
- PDB
- 4NHL
- Type
- protein
- Length
- 546 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
- OGA, MN
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pkhd-type hydroxylase TPA1 (EC 1.14.11.-) | protein | 546 | 31% helix, 26% strand | P40032 |
Ligands and binding sites
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 | 244 | 0.69 | 0.85 | 34 | empty |
| 2 | 133 | 0.63 | 0.86 | 28 | empty |
| 3 | 227 | 0.56 | 0.78 | 30 | OGA |
| 4 | 119 | 0.49 | 0.79 | 20 | empty |
| 5 | 67 | 0.37 | 0.78 | 14 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4NHL · Crystal structure of Tpa1p from Saccharomyces cerevisiae, termination and polyadenylation… · 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 4NHL · PDBe 4NHL · UniProt P40032
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