Research workbench
Crystal structure of arabidopsis thaliana phosphoserine aminotransferase isoform 1 (ATPSAT1) in complex with pyridoxamine-5'- phosphate (pmp)
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
- 6CZY
- Type
- protein
- Length
- 1,445 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
- PMP, NA, SO4
- Pockets
- 15 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoserine aminotransferase 1, chloroplastic (EC 2.6.1.52) | protein | 362 | 40% helix, 17% strand | Q96255 |
| B, C, D | Phosphoserine aminotransferase 1, chloroplastic (EC 2.6.1.52) | protein | 361 | 41% helix, 17% strand | Q96255 |
Ligands and binding sites
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 577 | 0.71 | 0.80 | 64 | empty |
| 2 | 470 | 0.70 | 0.81 | 71 | PMP |
| 3 | 664 | 0.70 | 0.77 | 84 | empty |
| 4 | 51 | 0.69 | 0.98 | 26 | empty |
| 5 | 334 | 0.67 | 0.81 | 42 | MPD, PMP |
Interfaces
6 interfaces between chains.
- A–B · 2479 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 2431 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 249 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 236 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 161 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6CZY · Crystal structure of Arabidopsis thaliana phosphoserine aminotransferase isoform 1… · the same entry in another collection · chain A against A, TM-score 1.00
- Q96255 · AlphaFold monomer V2.0 prediction for phosphoserine aminotransferase 1, chloroplastic… · a predicted model of the same protein · chain B 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 6CZY · PDBe 6CZY · UniProt Q96255
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