Research workbench
Crystal structure of serine hydroxymethyltransferase from psychromonas ingrahamii
Analyse Crystal structure of serine hydroxymethyltransferase from psychromonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P3M
- Type
- protein
- Length
- 765 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase
- EC
- 2.1.2.1
- UniProt
- A1SUU0
- Ligands
- SO4, CL
- Pockets
- 10 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 376 | 51% helix, 15% strand | A1SUU0 |
| B | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 389 | 50% helix, 15% strand | A1SUU0 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 7 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 406 | 0.59 | 0.75 | 50 | SO4 |
| 2 | 259 | 0.48 | 0.73 | 27 | empty |
| 3 | 124 | 0.47 | 0.79 | 21 | empty |
| 4 | 101 | 0.47 | 0.80 | 21 | GOL |
| 5 | 182 | 0.46 | 0.75 | 38 | SO4 |
Interfaces
1 interface between chains.
- A–B · 4088 Ų buried · 55 hydrogen bonds · protein-protein
Compared structures
- 4P3M · Crystal structure of serine hydroxymethyltransferase from Psychromonas ingrahamii · the same entry in another collection · chain A against A, TM-score 1.00
- A1SUU0 · AlphaFold monomer V2.0 prediction for serine hydroxymethyltransferase (A1SUU0) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 A1SUU0
- Elsewhere: RCSB PDB 4P3M · PDBe 4P3M · UniProt A1SUU0
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