Research workbench
Human SHMT2 in complex with pemetrexed
Analyse Human SHMT2 in complex with pemetrexed in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QVL
- Type
- protein
- Length
- 907 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.28
- Source
- Homo sapiens
- Molecule
- Serine hydroxymethyltransferase, mitochondrial
- EC
- 2.1.2.1
- UniProt
- P34897
- Ligands
- PLP, 4DW, CA
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.28 · 2 distinct chains · 49% 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 | 49% helix, 14% strand | P34897 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- 4DW · N-{4-[2-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)ethyl]benzoyl}-L-glutamic acid · ligand · chains A, B
- CA · Calcium ion · metal · chains A
- GOL · Glycerol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.74 | 0.98 | 17 | empty |
| 2 | 383 | 0.73 | 0.84 | 46 | 4DW |
| 3 | 340 | 0.68 | 0.82 | 46 | PLP |
| 4 | 50 | 0.42 | 0.84 | 16 | empty |
| 5 | 72 | 0.40 | 0.79 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 4662 Ų buried · 67 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 6QVL · PDBe 6QVL · UniProt P34897
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