Research workbench
Crystal structure of smt fusion peptidyl-prolyl cis-trans isomerase from burkholderia pseudomallei complexed with SF354
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
- 5V8T
- Type
- protein
- Length
- 382 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, A0A069BB90
- Ligands
- 8ZV, MG
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ubiquitin-like protein SMT3,PEPTIDYL-prolyl cis-trans isomerase (EC 5.2.1.8) | protein | 191 | 13% helix, 38% strand | Q12306, A0A069BB90 |
Ligands and binding sites
- 8ZV · 2-{[3,5-bis(2-methoxyethoxy)benzene-1-carbonyl]amino}ethyl (2S)-1-(benzylsulfonyl) piperidine-2-carboxylate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A, B
- FMT · Formic acid · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 686 | 0.71 | 0.77 | 42 | 8ZV |
| 2 | 261 | 0.60 | 0.79 | 24 | empty |
| 3 | 139 | 0.56 | 0.82 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 317 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5V8T · 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 A0A069BB90
- Elsewhere: RCSB PDB 5V8T · PDBe 5V8T · UniProt Q12306 · UniProt A0A069BB90
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