MolNFT v1 · #98050 · protein
Alanine-glyoxylate aminotransferase variant K390A/K391A in complex with the tpr domain of human PEX5P
4KXK · Serine--pyruvate aminotransferase: “Alanine-glyoxylate aminotransferase variant K390A/K391A in complex with the tpr domain of human PEX5P”. X-ray diffraction, 1 ligand (SO4), 12 pockets (best druggability 0.64). MolNFT v1 #98050 on…
- PDB
- 4KXK
- Type
- protein
- Length
- 1,350 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine--pyruvate aminotransferase; Peroxisomal targeting signal 1 receptor
- EC
- 2.6.1.51, 2.6.1.44
- UniProt
- P21549, P50542
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Serine--pyruvate aminotransferase (EC 2.6.1.51, 2.6.1.44) | protein | 387 | 41% helix, 15% strand | P21549 |
| B, D | Peroxisomal targeting signal 1 receptor | protein | 288 | 72% helix, 0% strand | P50542 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.64 | 0.82 | 30 | empty |
| 2 | 444 | 0.63 | 0.77 | 52 | empty |
| 3 | 260 | 0.62 | 0.80 | 40 | SO4, BME |
| 4 | 241 | 0.61 | 0.81 | 29 | empty |
| 5 | 328 | 0.61 | 0.78 | 43 | SO4 |
Interfaces
3 interfaces between chains.
- A–C · 4068 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 981 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 959 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4KXK · Alanine-glyoxylate aminotransferase variant K390A/K391A in complex with the TPR domain of… · the same entry in another collection · chain B against B, TM-score 1.00
- P21549 · AlphaFold monomer V2.0 prediction for serine--pyruvate aminotransferase (P21549) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P50542 · AlphaFold monomer V2.0 prediction for peroxisomal targeting signal 1 receptor (P50542) · a predicted model of the same protein · chain B 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 P21549
- Every structure of UniProt P50542
- Elsewhere: RCSB PDB 4KXK · PDBe 4KXK · UniProt P21549 · UniProt P50542
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