MolNFT v1 · #161998 · protein
Human SHMT2 in complex with lometrexol
6QVG · Serine hydroxymethyltransferase, mitochondrial: “Human SHMT2 in complex with lometrexol”. X-ray diffraction, 4 ligands (DDF, PLP, GLY), 15 pockets (best druggability 0.75). MolNFT v1 #161998 on GenesisL1: 3D structure, binding sites…
- PDB
- 6QVG
- Type
- protein
- Length
- 907 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
- DDF, PLP, GLY, NA
- Pockets
- 15 · best druggability 0.75
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 | 453 | 50% helix, 14% strand | P34897 |
| B | Serine hydroxymethyltransferase, mitochondrial (EC 2.1.2.1) | protein | 454 | 50% helix, 14% strand | P34897 |
Ligands and binding sites
- DDF · 5,10-dideazatetrahydrofolic acid · ligand · 2 copies · chains A, B
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- GLY · Glycine · ligand · chains A, B
- NA · Sodium ion · metal · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.75 | 0.98 | 18 | GOL |
| 2 | 357 | 0.70 | 0.83 | 35 | DDF |
| 3 | 320 | 0.67 | 0.81 | 28 | DDF |
| 4 | 51 | 0.43 | 0.84 | 18 | empty |
| 5 | 69 | 0.39 | 0.79 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 4616 Ų buried · 66 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
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 6QVG · PDBe 6QVG · UniProt P34897
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