MolNFT v1 · #166678 · protein
Structure of serine hydroxymethyltransferase 8 from glycine max cultivar essex complexed with plp-glycine and 5- formyltetrahydrofolate
6UXJ: “Structure of serine hydroxymethyltransferase 8 from glycine max cultivar essex complexed with plp-glycine and…”. X-ray diffraction, 2 ligands (PLG, FFO), 20 pockets (best druggability 0.81). MolNFT v1 #166678 on GenesisL1: 3D…
- PDB
- 6UXJ
- Type
- protein
- Length
- 1,887 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase
- EC
- 2.1.2.1
- UniProt
- K4FZF8
- Ligands
- PLG, FFO
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 471 | 47% helix, 13% strand | K4FZF8 |
| B, D | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 472 | 48% helix, 13% strand | K4FZF8 |
| C | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 472 | 47% helix, 13% strand | K4FZF8 |
Ligands and binding sites
- PLG · N-glycine-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-yl-methane] · ligand · 4 copies · chains A, B, C, D
- FFO · N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 352 | 0.81 | 0.91 | 58 | PLG, FFO, EDO |
| 2 | 372 | 0.80 | 0.89 | 64 | PLG, FFO, EDO |
| 3 | 424 | 0.79 | 0.88 | 66 | PLG, FFO, EDO |
| 4 | 83 | 0.78 | 0.99 | 15 | EDO |
| 5 | 575 | 0.78 | 0.84 | 88 | PLG, FFO, EDO |
Interfaces
6 interfaces between chains.
- A–B · 4929 Ų buried · 61 hydrogen bonds · protein-protein
- C–D · 4918 Ų buried · 61 hydrogen bonds · protein-protein
- A–C · 797 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 778 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 26 Ų buried · 0 hydrogen bonds · protein-protein
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 K4FZF8
- Elsewhere: RCSB PDB 6UXJ · PDBe 6UXJ · UniProt K4FZF8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.