MolNFT v1 · #92775 · protein
Crystal structure of a smt fusion peptidyl-prolyl cis-trans isomerase with surface mutation D44G from burkholderia pseudomallei complexed with CJ183
4GIV · 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 (4GI), 3 pockets (best druggability…
- PDB
- 4GIV
- Type
- protein
- Length
- 376 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
- 4GI
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 38% 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 | 192 | 14% helix, 37% strand | Q12306, Q3JK38 |
| B | Ubiquitin-like protein SMT3, peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) | protein | 184 | 13% helix, 38% strand | Q12306, Q3JK38 |
Ligands and binding sites
- 4GI · 3-(pyridin-3-yl)propyl (2S)-1-[(3-nitrophenyl)sulfonyl]piperidine-2-carboxylate · ligand · 2 copies · chains A, B
- FMT · Formic acid · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 730 | 0.78 | 0.82 | 47 | 4GI |
| 2 | 318 | 0.56 | 0.75 | 33 | empty |
| 3 | 211 | 0.50 | 0.76 | 29 | FMT |
Interfaces
1 interface between chains.
- A–B · 715 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4GIV · 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 0.40
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 4GIV · PDBe 4GIV · UniProt Q12306 · UniProt Q3JK38
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