Research workbench
Human alanine-glyoxylate aminotransferase in complex with the tpr domain of human PEX5P
Analyse Human alanine-glyoxylate aminotransferase in complex with the tpr domain of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R9A
- Type
- protein
- Length
- 1,357 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
- Pockets
- 14 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine--pyruvate aminotransferase (EC 2.6.1.51, 2.6.1.44) | protein | 387 | 42% helix, 14% strand | P21549 |
| B | Peroxisomal targeting signal 1 receptor | protein | 289 | 71% helix, 0% strand | P50542 |
| C | Serine--pyruvate aminotransferase (EC 2.6.1.51, 2.6.1.44) | protein | 389 | 40% helix, 15% strand | P21549 |
| D | Peroxisomal targeting signal 1 receptor | protein | 292 | 72% helix, 0% strand | P50542 |
Ligands and binding sites
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.64 | 0.77 | 47 | empty |
| 2 | 238 | 0.63 | 0.81 | 31 | empty |
| 3 | 273 | 0.61 | 0.80 | 31 | empty |
| 4 | 260 | 0.59 | 0.79 | 38 | empty |
| 5 | 134 | 0.54 | 0.82 | 26 | empty |
Interfaces
4 interfaces between chains.
- A–C · 4222 Ų buried · 54 hydrogen bonds · protein-protein
- C–D · 1098 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1008 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 34 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cofactor).
Compared structures
- 3R9A · Human alanine-glyoxylate aminotransferase in complex with the TPR domain of human PEX5P · the same entry in another collection · chain D against D, 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 0.98
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 3R9A · PDBe 3R9A · UniProt P21549 · UniProt P50542
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