MolNFT v1 · #109256 · protein
Crystal structure of serine hydroxymethyltransferase from streptococcus thermophilus
4WXB: “Crystal structure of serine hydroxymethyltransferase from streptococcus thermophilus”. X-ray diffraction, 1 ligand (NA), 20 pockets (best druggability 0.83). MolNFT v1 #109256 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4WXB
- Type
- protein
- Length
- 1,620 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase
- EC
- 2.1.2.1
- UniProt
- Q5M0B4
- Ligands
- NA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 410 | 47% helix, 13% strand | Q5M0B4 |
| B, C | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 400 | 49% helix, 14% strand | Q5M0B4 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains B, C, D
- CIT · Citric acid · additive · 4 copies · chains A, C, B, D
- CAC · Cacodylate ion · additive · 4 copies · chains A, C, B, D
- GOL · Glycerol · additive · 4 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 | 997 | 0.83 | 0.84 | 101 | empty |
| 2 | 668 | 0.81 | 0.85 | 92 | CIT, CAC |
| 3 | 770 | 0.78 | 0.82 | 81 | CIT, CAC |
| 4 | 523 | 0.76 | 0.84 | 64 | CIT, CAC |
| 5 | 670 | 0.72 | 0.79 | 51 | CIT, CAC |
Interfaces
3 interfaces between chains.
- A–C · 3309 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 3279 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 752 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4WXB · Crystal Structure of Serine Hydroxymethyltransferase from Streptococcus thermophilus · the same entry in another collection · chain A against A, TM-score 1.00
- Q5M0B4 · AlphaFold monomer V2.0 prediction for serine hydroxymethyltransferase (Q5M0B4) · 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 Q5M0B4
- Elsewhere: RCSB PDB 4WXB · PDBe 4WXB · UniProt Q5M0B4
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