Research workbench
Crystal structure of arabidopsis thaliana phosphoserine aminotransferase isoform 1 (ATPSAT1) in complex with plp- phosphoserine geminal diamine intermediate
Analyse Crystal structure of arabidopsis thaliana phosphoserine aminotransferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CZZ
- Type
- protein
- Length
- 1,440 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoserine aminotransferase 1, chloroplastic
- EC
- 2.6.1.52
- UniProt
- Q96255
- Ligands
- PLP, SEP, NA
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Phosphoserine aminotransferase 1, chloroplastic (EC 2.6.1.52) | protein | 360 | 42% helix, 17% strand | Q96255 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- SEP · Phosphoserine · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 948 | 0.75 | 0.78 | 85 | empty |
| 2 | 50 | 0.70 | 0.98 | 29 | empty |
| 3 | 248 | 0.69 | 0.85 | 41 | PLP, SEP |
| 4 | 218 | 0.68 | 0.86 | 37 | PLP, SEP |
| 5 | 231 | 0.68 | 0.85 | 42 | PLP, SEP |
Interfaces
3 interfaces between chains.
- C–D · 2520 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 2517 Ų buried · 40 hydrogen bonds · protein-protein
- A–D · 337 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6CZZ · Crystal structure of Arabidopsis thaliana phosphoserine aminotransferase isoform 1… · the same entry in another collection · chain D against D, TM-score 1.00
- Q96255 · AlphaFold monomer V2.0 prediction for phosphoserine aminotransferase 1, chloroplastic… · a predicted model of the same protein · chain C 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 Q96255
- Elsewhere: RCSB PDB 6CZZ · PDBe 6CZZ · UniProt Q96255
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