Research workbench
Structure of aminoacid racemase in complex with plp
Analyse Structure of aminoacid racemase in complex with plp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YSN
- Type
- protein
- Length
- 1,779 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative 4-aminobutyrate aminotransferase
- UniProt
- M1GRN3
- Ligands
- PLP
- Pockets
- 16 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative 4-aminobutyrate aminotransferase | protein | 446 | 42% helix, 18% strand | M1GRN3 |
| B | Putative 4-aminobutyrate aminotransferase | protein | 443 | 43% helix, 18% strand | M1GRN3 |
| C | Putative 4-aminobutyrate aminotransferase | protein | 448 | 43% helix, 18% strand | M1GRN3 |
| D | Putative 4-aminobutyrate aminotransferase | protein | 442 | 42% helix, 18% strand | M1GRN3 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 243 | 0.84 | 0.96 | 42 | empty |
| 2 | 237 | 0.84 | 0.96 | 43 | empty |
| 3 | 683 | 0.75 | 0.81 | 83 | PLP |
| 4 | 60 | 0.72 | 0.98 | 25 | PLP |
| 5 | 64 | 0.72 | 0.98 | 29 | PLP |
Interfaces
6 interfaces between chains.
- A–B · 5225 Ų buried · 82 hydrogen bonds · protein-protein
- C–D · 5178 Ų buried · 79 hydrogen bonds · protein-protein
- B–C · 1309 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1308 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 94 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
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 M1GRN3
- Elsewhere: RCSB PDB 4YSN · PDBe 4YSN · UniProt M1GRN3
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