MolNFT v1 · #92707 · protein
Crystal structure of a smt fusion peptidyl-prolyl cis-trans isomerase from burkholderia pseudomallei complexed with CJ40
4GGQ · Ubiquitin-like protein SMT3, peptidyl-prolyl cis-trans…: “Crystal structure of a smt fusion peptidyl-prolyl cis-trans isomerase from burkholderia pseudomallei…”. X-ray diffraction, 2 ligands (861, CA), 10 pockets (best druggability…
- PDB
- 4GGQ
- Type
- protein
- Length
- 744 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
- 861, CA
- Pockets
- 10 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A | Ubiquitin-like protein SMT3, peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) | protein | 191 | 14% helix, 39% strand | Q12306, Q3JK38 |
| B | Ubiquitin-like protein SMT3, peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) | protein | 185 | 14% helix, 39% strand | Q12306, Q3JK38 |
| D | Ubiquitin-like protein SMT3, peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) | protein | 177 | 13% helix, 39% strand | Q12306, Q3JK38 |
Ligands and binding sites
- 861 · 3-(3,4,5-trimethoxyphenyl)propyl (2S)-1-(benzylsulfonyl)piperidine-2-carboxylate · ligand · 4 copies · chains C, A, B, D
- CA · Calcium ion · metal · 2 copies · chains C, A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.52 | 0.76 | 34 | empty |
| 2 | 231 | 0.51 | 0.76 | 23 | empty |
| 3 | 237 | 0.51 | 0.75 | 22 | empty |
| 4 | 141 | 0.42 | 0.75 | 25 | empty |
| 5 | 74 | 0.38 | 0.77 | 14 | 861 |
Interfaces
4 interfaces between chains.
- C–A · 396 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 227 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 177 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 77 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4GGQ · Crystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase from Burkholderia… · the same entry in another collection · chain C against C, TM-score 1.00
- Q12306 · AlphaFold monomer V2.0 prediction for ubiquitin-like protein SMT3 (Q12306) · a predicted model of the same protein · chain C 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 4GGQ · PDBe 4GGQ · UniProt Q12306 · UniProt Q3JK38
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