Research workbench
A. thaliana serine hydroxymethyltransferase isoform 4 (ATSHMT4) in complex with methotrexate
Analyse A. thaliana serine hydroxymethyltransferase isoform 4 (ATSHMT4) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SMR
- Type
- protein
- Length
- 1,887 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase 4
- EC
- 2.1.2.1
- UniProt
- O23254
- Ligands
- PLS, MTX
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine hydroxymethyltransferase 4 (EC 2.1.2.1) | protein | 473 | 49% helix, 14% strand | O23254 |
| B | Serine hydroxymethyltransferase 4 (EC 2.1.2.1) | protein | 472 | 49% helix, 13% strand | O23254 |
| C, D | Serine hydroxymethyltransferase 4 (EC 2.1.2.1) | protein | 471 | 48% helix, 13% strand | O23254 |
Ligands and binding sites
- PLS · [3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl]-serine · ligand · 4 copies · chains A, B, C, D
- MTX · Methotrexate · ligand · 3 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, D, B, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 689 | 0.79 | 0.84 | 88 | PLS, MTX |
| 2 | 682 | 0.79 | 0.84 | 86 | PLS, MTX |
| 3 | 89 | 0.78 | 0.98 | 15 | empty |
| 4 | 82 | 0.78 | 0.99 | 14 | empty |
| 5 | 611 | 0.76 | 0.82 | 69 | MTX, PLS |
Interfaces
6 interfaces between chains.
- A–B · 4935 Ų buried · 57 hydrogen bonds · protein-protein
- C–D · 4908 Ų buried · 57 hydrogen bonds · protein-protein
- B–C · 813 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 795 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 27 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- O23254 · AlphaFold monomer V2.0 prediction for serine hydroxymethyltransferase 4 (O23254) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 O23254
- Elsewhere: RCSB PDB 6SMR · PDBe 6SMR · UniProt O23254
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.