Research workbench
Structure of human SHMT1-H135N-R137A-E168N mutant at 3.6 ang. resolution
Analyse Structure of human SHMT1-H135N-R137A-E168N mutant at 3.6 ang. resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FL5
- Type
- protein
- Length
- 1,866 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase, cytosolic
- EC
- 2.1.2.1
- UniProt
- P34896
- Ligands
- PLP, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine hydroxymethyltransferase, cytosolic (EC 2.1.2.1) | protein | 471 | 49% helix, 13% strand | P34896 |
| D | Serine hydroxymethyltransferase, cytosolic (EC 2.1.2.1) | protein | 470 | 49% helix, 14% strand | P34896 |
| G | Serine hydroxymethyltransferase, cytosolic (EC 2.1.2.1) | protein | 467 | 49% helix, 13% strand | P34896 |
| J | Serine hydroxymethyltransferase, cytosolic (EC 2.1.2.1) | protein | 458 | 49% helix, 14% strand | P34896 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, D, G, J
- CL · Chloride ion · ion · 4 copies · chains A, D, G, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 550 | 0.83 | 0.89 | 84 | CL, PLP |
| 2 | 91 | 0.78 | 0.98 | 26 | empty |
| 3 | 850 | 0.77 | 0.80 | 113 | empty |
| 4 | 64 | 0.72 | 0.98 | 30 | empty |
| 5 | 481 | 0.71 | 0.81 | 52 | CL |
Interfaces
5 interfaces between chains.
- A–D · 4890 Ų buried · 60 hydrogen bonds · protein-protein
- G–J · 4560 Ų buried · 55 hydrogen bonds · protein-protein
- D–J · 880 Ų buried · 15 hydrogen bonds · protein-protein
- A–G · 867 Ų buried · 13 hydrogen bonds · protein-protein
- A–J · 13 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6FL5 · Structure of human SHMT1-H135N-R137A-E168N mutant at 3.6 Ang. resolution · the same entry in another collection · chain J against J, TM-score 1.00
- P34896 · AlphaFold monomer V2.0 prediction for serine hydroxymethyltransferase, cytosolic (P34896) · a predicted model of the same protein · chain G 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 P34896
- Elsewhere: RCSB PDB 6FL5 · PDBe 6FL5 · UniProt P34896
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