Research workbench
Crystal structure of TPA1 from saccharomyces cerevisiae, a component of the messenger ribonucleoprotein complex
Analyse Crystal structure of TPA1 from saccharomyces cerevisiae, a component of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KT1
- Type
- protein
- Length
- 557 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
- FE, SO4
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pkhd-type hydroxylase TPA1 (EC 1.14.11.-) | protein | 557 | 30% helix, 25% strand | P40032 |
Ligands and binding sites
- FE · Fe (III) ion · metal · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 255 | 0.67 | 0.84 | 41 | empty |
| 2 | 166 | 0.64 | 0.85 | 31 | empty |
| 3 | 93 | 0.46 | 0.80 | 19 | empty |
| 4 | 155 | 0.41 | 0.73 | 22 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3KT1 · Crystal structure of Tpa1 from Saccharomyces cerevisiae, a component of the messenger… · 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 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 P40032
- Elsewhere: RCSB PDB 3KT1 · PDBe 3KT1 · UniProt P40032
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