MolNFT v1 · #139071 · protein
Structure of human SHMT2 protein mutant
5X3V · Serine hydroxymethyltransferase, mitochondrial: “Structure of human SHMT2 protein mutant”. X-ray diffraction, 1 ligand (SO4), 10 pockets (best druggability 0.80). MolNFT v1 #139071 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5X3V
- Type
- protein
- Length
- 887 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
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine hydroxymethyltransferase, mitochondrial (EC 2.1.2.1) | protein | 445 | 48% helix, 12% strand | P34897 |
| B | Serine hydroxymethyltransferase, mitochondrial (EC 2.1.2.1) | protein | 442 | 48% helix, 11% strand | P34897 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 804 | 0.80 | 0.83 | 98 | SO4 |
| 2 | 660 | 0.79 | 0.84 | 64 | SO4 |
| 3 | 95 | 0.58 | 0.86 | 20 | empty |
| 4 | 91 | 0.57 | 0.86 | 24 | empty |
| 5 | 116 | 0.43 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 4695 Ų buried · 66 hydrogen bonds · protein-protein
Compared structures
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 5X3V · PDBe 5X3V · UniProt P34897
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