Research workbench
Crystal structure of smt fusion peptidyl-prolyl cis-trans isomerase from burkholderia pseudomallei complexed with SF339
Analyse Crystal structure of smt fusion peptidyl-prolyl cis-trans isomerase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O49
- Type
- protein
- Length
- 380 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
- LL7, CA
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 13% 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 | 13% helix, 40% strand | Q12306, Q3JK38 |
| B | Ubiquitin-like protein SMT3,PEPTIDYL-prolyl cis-trans isomerase (EC 5.2.1.8) | protein | 189 | 12% helix, 39% strand | Q12306, Q3JK38 |
Ligands and binding sites
- LL7 · (2~{S})-~{N}-[3-oxidanylidene-3-[(3,4,5-trimethoxyphenyl)amino]propyl]-1-(phenylmethyl) sulfonyl-piperidine-2-carboxamide · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 577 | 0.65 | 0.75 | 40 | LL7 |
| 2 | 384 | 0.64 | 0.78 | 34 | empty |
| 3 | 146 | 0.47 | 0.77 | 25 | empty |
| 4 | 53 | 0.39 | 0.81 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 252 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6O49 · Crystal structure of smt fusion peptidyl-prolyl cis-trans isomerase from burkholderia… · 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 B 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 6O49 · PDBe 6O49 · UniProt Q12306 · UniProt Q3JK38
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