MolNFT v1 · #124669 · protein
Crystal structure of smt fusion peptidyl-prolyl cis-trans isomerase from burkholderia pseudomallei complexed with SF110
5KLX · Chimera protein of ubiquitin-like protein SMT3 and…: “Crystal structure of smt fusion peptidyl-prolyl cis-trans isomerase from burkholderia pseudomallei complexed…”. X-ray diffraction, 2 ligands (6UO, MG), 8 pockets (best…
- PDB
- 5KLX
- Type
- protein
- Length
- 734 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chimera protein of ubiquitin-like protein SMT3 and peptidyl-prolyl cis-trans isomerase
- EC
- 5.2.1.8
- UniProt
- Q12306, Q3JK38
- Ligands
- 6UO, MG
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chimera protein of ubiquitin-like protein SMT3 and peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) | protein | 186 | 13% helix, 38% strand | Q12306, Q3JK38 |
| B | Chimera protein of ubiquitin-like protein SMT3 and peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) | protein | 180 | 17% helix, 36% strand | Q12306, Q3JK38 |
| C | Chimera protein of ubiquitin-like protein SMT3 and peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) | protein | 183 | 15% helix, 37% strand | Q12306, Q3JK38 |
| D | Chimera protein of ubiquitin-like protein SMT3 and peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) | protein | 185 | 10% helix, 38% strand | Q12306, Q3JK38 |
Ligands and binding sites
- 6UO · 2-[(2~{S})-1-(phenylmethyl)sulfonylpiperidin-2-yl]carbonyloxyethyl pyridine-3-carboxylate · ligand · 4 copies · chains A, B, D, C
- MG · Magnesium ion · metal · 2 copies · chains A, B, D
- IMD · Imidazole · additive · 2 copies · chains A, D
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 689 | 0.75 | 0.80 | 44 | 6UO |
| 2 | 342 | 0.64 | 0.79 | 46 | empty |
| 3 | 282 | 0.54 | 0.76 | 29 | empty |
| 4 | 277 | 0.54 | 0.76 | 28 | IMD |
| 5 | 140 | 0.40 | 0.74 | 23 | empty |
Interfaces
4 interfaces between chains.
- B–D · 541 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 215 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 94 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 76 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5KLX · Crystal Structure of SMT Fusion Peptidyl-Prolyl Cis-Trans Isomerase from Burkholderia… · the same entry in another collection · chain D against D, 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 5KLX · PDBe 5KLX · UniProt Q12306 · UniProt Q3JK38
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