Research workbench
Crystal structure of serine hydroxymethyltransferase, isoform 2 from Arabidopsis thaliana (SHM2)
Analyse Crystal structure of serine hydroxymethyltransferase, isoform 2 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PZZ
- Type
- protein
- Length
- 1,902 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.65
- Source
- Arabidopsis thaliana
- Molecule
- Serine hydroxymethyltransferase 2, mitochondrial
- EC
- 2.1.2.1
- UniProt
- Q94C74
- Ligands
- CL, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · resolution 1.65 · 4 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine hydroxymethyltransferase 2, mitochondrial (EC 2.1.2.1) | protein | 475 | 50% helix, 14% strand | Q94C74 |
| B | Serine hydroxymethyltransferase 2, mitochondrial (EC 2.1.2.1) | protein | 474 | 51% helix, 14% strand | Q94C74 |
| C | Serine hydroxymethyltransferase 2, mitochondrial (EC 2.1.2.1) | protein | 473 | 51% helix, 14% strand | Q94C74 |
| D | Serine hydroxymethyltransferase 2, mitochondrial (EC 2.1.2.1) | protein | 480 | 51% helix, 15% strand | Q94C74 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains C
- EDO · 1,2-ethanediol · additive · 28 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains C, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1131 | 0.80 | 0.81 | 122 | EDO |
| 2 | 1103 | 0.76 | 0.78 | 126 | EDO |
| 3 | 430 | 0.75 | 0.84 | 32 | EDO, CL |
| 4 | 414 | 0.74 | 0.84 | 35 | EDO, CL |
| 5 | 59 | 0.74 | 0.99 | 14 | empty |
Interfaces
6 interfaces between chains.
- C–D · 4981 Ų buried · 67 hydrogen bonds · protein-protein
- A–B · 4910 Ų buried · 60 hydrogen bonds · protein-protein
- B–C · 814 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 782 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 46 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 7PZZ · Crystal structure of serine hydroxymethyltransferase, isoform 2 from arabidopsis thaliana… · the same entry in another collection · chain D against D, TM-score 1.00
- Q94C74 · AlphaFold monomer V2.0 prediction for serine hydroxymethyltransferase 2, mitochondrial… · a predicted model of the same protein · chain A 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 Q94C74
- Elsewhere: RCSB PDB 7PZZ · PDBe 7PZZ · UniProt Q94C74
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