Research workbench
Alanine-glyoxylate aminotransferase variant K390A in complex with the tpr domain of human PEX5P
Analyse Alanine-glyoxylate aminotransferase variant K390A in complex with the tpr… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KYO
- Type
- protein
- Length
- 1,346 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
- 13 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 55% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine-pyruvate aminotransferase (EC 2.6.1.51, 2.6.1.44) | protein | 387 | 41% helix, 15% strand | P21549 |
| C | Serine-pyruvate aminotransferase (EC 2.6.1.51, 2.6.1.44) | protein | 388 | 41% helix, 15% strand | P21549 |
| B | Peroxisomal targeting signal 1 receptor | protein | 286 | 71% helix, 0% strand | P50542 |
| D | Peroxisomal targeting signal 1 receptor | protein | 285 | 74% helix, 0% strand | P50542 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
- BME · Beta-mercaptoethanol · additive · 12 copies · chains A, C, B, D
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.67 | 0.80 | 52 | SO4, BME |
| 2 | 313 | 0.66 | 0.81 | 51 | SO4, BME |
| 3 | 227 | 0.63 | 0.82 | 31 | BME |
| 4 | 225 | 0.63 | 0.82 | 33 | empty |
| 5 | 282 | 0.52 | 0.75 | 34 | empty |
Interfaces
3 interfaces between chains.
- A–C · 4055 Ų buried · 48 hydrogen bonds · protein-protein
- C–D · 1022 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 984 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 4KYO · Alanine-glyoxylate aminotransferase variant K390A in complex with the TPR domain of human… · the same entry in another collection · chain C against C, TM-score 1.00
- P21549 · AlphaFold monomer V2.0 prediction for serine--pyruvate aminotransferase (P21549) · a predicted model of the same protein · chain C 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 D 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 4KYO · PDBe 4KYO · UniProt P21549 · UniProt P50542
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