Research workbench
Crystal structure of rabbit cytosolic serine hydroxymethyltransferase at 2.8 ångström resolution
Analyse Crystal structure of rabbit cytosolic serine hydroxymethyltransferase at 2.8… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1CJ0
- Type
- protein
- Length
- 930 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (serine hydroxymethyltransferase)
- UniProt
- P07511
- Ligands
- PLP
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (serine hydroxymethyltransferase) | protein | 464 | 47% helix, 13% strand | P07511 |
| B | Protein (serine hydroxymethyltransferase) | protein | 466 | 47% helix, 14% strand | P07511 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.75 | 0.98 | 16 | empty |
| 2 | 322 | 0.70 | 0.83 | 28 | empty |
| 3 | 264 | 0.65 | 0.82 | 27 | empty |
| 4 | 112 | 0.47 | 0.80 | 34 | empty |
| 5 | 119 | 0.44 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 4550 Ų buried · 53 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1CJ0 · Crystal structure of rabbit cytosolic serine hydroxymethyltransferase at 2.8 ångström… · the same entry in another collection · chain A against A, TM-score 1.00
- P07511 · AlphaFold monomer V2.0 prediction for serine hydroxymethyltransferase, cytosolic (P07511) · 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 P07511
- Elsewhere: RCSB PDB 1CJ0 · PDBe 1CJ0 · UniProt P07511
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