MolNFT v1 · #92353 · protein
Crystal structure of a smt fusion peptidyl-prolyl cis-trans isomerase with surface mutation D44G from burkholderia pseudomallei complexed with CJ168
4G50 · Ubiquitin-like protein SMT3, peptidyl-prolyl cis-trans…: “Crystal structure of a smt fusion peptidyl-prolyl cis-trans isomerase with surface mutation D44G from…”. X-ray diffraction, 1 ligand (861), 6 pockets (best druggability…
- PDB
- 4G50
- Type
- protein
- Length
- 381 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-like protein SMT3, peptidyl-prolyl cis-trans isomerase
- EC
- 5.2.1.8
- UniProt
- Q12306, Q3JK38
- Ligands
- 861
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-like protein SMT3, peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) | protein | 191 | 12% helix, 39% strand | Q12306, Q3JK38 |
| B | Ubiquitin-like protein SMT3, peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) | protein | 190 | 12% helix, 38% strand | Q12306, Q3JK38 |
Ligands and binding sites
- 861 · 3-(3,4,5-trimethoxyphenyl)propyl (2S)-1-(benzylsulfonyl)piperidine-2-carboxylate · ligand · 2 copies · chains A, B
- FMT · Formic acid · additive · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.62 | 0.83 | 31 | empty |
| 2 | 69 | 0.51 | 0.85 | 17 | empty |
| 3 | 89 | 0.40 | 0.77 | 18 | empty |
| 4 | 89 | 0.39 | 0.76 | 16 | 861 |
| 5 | 73 | 0.36 | 0.76 | 15 | 861 |
Interfaces
1 interface between chains.
- A–B · 311 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4G50 · Crystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase with surface… · the same entry in another collection · chain A against A, TM-score 1.00
- Q12306 · AlphaFold monomer V2.0 prediction for ubiquitin-like protein SMT3 (Q12306) · a predicted model of the same protein · chain A against A, TM-score 0.41
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 Q12306
- Every structure of UniProt Q3JK38
- Elsewhere: RCSB PDB 4G50 · PDBe 4G50 · UniProt Q12306 · UniProt Q3JK38
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