MolNFT v1 · #158777 · protein
Crystal structure of smt fusion peptidyl-prolyl cis-trans isomerase from burkholderia pseudomallei complexed with SF355
6O4A · Ubiquitin-like protein SMT3,PEPTIDYL-prolyl cis-trans…: “Crystal structure of smt fusion peptidyl-prolyl cis-trans isomerase from burkholderia pseudomallei complexed…”. X-ray diffraction, 2 ligands (LLD, CA), 9 pockets (best…
- PDB
- 6O4A
- Type
- protein
- Length
- 760 residues
- Chains
- 4
- 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
- LLD, CA
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ubiquitin-like protein SMT3,PEPTIDYL-prolyl cis-trans isomerase (EC 5.2.1.8) | protein | 189 | 12% helix, 38% strand | Q12306, Q3JK38 |
| B, D | Ubiquitin-like protein SMT3,PEPTIDYL-prolyl cis-trans isomerase (EC 5.2.1.8) | protein | 191 | 12% helix, 38% strand | Q12306, Q3JK38 |
Ligands and binding sites
- LLD · 2-(pyridin-3-ylcarbonylamino)ethyl (2~{S})-1-(phenylmethyl)sulfonylpiperidine-2-carboxylate · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 692 | 0.80 | 0.84 | 43 | LLD |
| 2 | 861 | 0.80 | 0.82 | 67 | LLD |
| 3 | 357 | 0.61 | 0.77 | 39 | empty |
| 4 | 334 | 0.60 | 0.77 | 35 | empty |
| 5 | 246 | 0.55 | 0.77 | 27 | empty |
Interfaces
4 interfaces between chains.
- A–B · 689 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 688 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 190 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 119 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6O4A · 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 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 6O4A · PDBe 6O4A · UniProt Q12306 · UniProt Q3JK38
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