Research workbench
Crystal structure of homo sapiens holo serine hydroxymethyltransferase 2 (mitochondrial) (SHMT2), isoform 3, transcript variant 5, 483 aa, at 2.6 ang. resolution
Analyse Crystal structure of homo sapiens holo serine hydroxymethyltransferase 2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PVF
- Type
- protein
- Length
- 901 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase, mitochondrial
- EC
- 2.1.2.1
- UniProt
- P34897
- Pockets
- 17 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine hydroxymethyltransferase, mitochondrial (EC 2.1.2.1) | protein | 454 | 50% helix, 14% strand | P34897 |
| B | Serine hydroxymethyltransferase, mitochondrial (EC 2.1.2.1) | protein | 447 | 51% helix, 14% strand | P34897 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.77 | 0.98 | 26 | empty |
| 2 | 313 | 0.68 | 0.82 | 31 | GOL |
| 3 | 239 | 0.65 | 0.83 | 25 | GOL |
| 4 | 69 | 0.49 | 0.85 | 22 | empty |
| 5 | 65 | 0.47 | 0.84 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 4670 Ų buried · 71 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cofactor).
Compared structures
- 4PVF · Crystal structure of Homo sapiens holo serine hydroxymethyltransferase 2 (mitochondrial)… · the same entry in another collection · chain A against A, TM-score 1.00
- P34897 · AlphaFold monomer V2.0 prediction for serine hydroxymethyltransferase, mitochondrial… · 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 P34897
- Elsewhere: RCSB PDB 4PVF · PDBe 4PVF · UniProt P34897
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