MolNFT v1 · #75124 · protein
Serine hydroxymethyltransferase from staphylococcus aureus, S95P mutant.
3PGY: “Serine hydroxymethyltransferase from staphylococcus aureus, S95P mutant.”. X-ray diffraction, 1 ligand (GLY), 20 pockets (best druggability 0.80). MolNFT v1 #75124 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3PGY
- Type
- protein
- Length
- 1,606 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase
- EC
- 2.1.2.1
- UniProt
- Q5HE87
- Ligands
- GLY
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 402 | 51% helix, 13% strand | Q5HE87 |
| B | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 404 | 52% helix, 14% strand | Q5HE87 |
| C | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 398 | 53% helix, 14% strand | Q5HE87 |
| D | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 402 | 51% helix, 14% strand | Q5HE87 |
Ligands and binding sites
- GLY · Glycine · ligand · 3 copies · chains A, B
- CIT · Citric acid · additive · 8 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 755 | 0.80 | 0.84 | 71 | CIT |
| 2 | 1003 | 0.79 | 0.80 | 74 | CIT |
| 3 | 906 | 0.77 | 0.80 | 71 | EDO, CIT |
| 4 | 848 | 0.75 | 0.79 | 76 | CIT |
| 5 | 180 | 0.61 | 0.83 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3542 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 3538 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 291 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 30 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 17 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3PGY · Serine hydroxymethyltransferase from Staphylococcus aureus, S95P mutant. · the same entry in another collection · chain D against D, TM-score 1.00
- Q5HE87 · AlphaFold monomer V2.0 prediction for serine hydroxymethyltransferase (Q5HE87) · a predicted model of the same protein · chain B 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 Q5HE87
- Elsewhere: RCSB PDB 3PGY · PDBe 3PGY · UniProt Q5HE87
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