Research workbench
The sanglifehrin-cyclophilin interaction: degradation work, synthetic macrocyclic analogues, X-ray crystal structure and binding data
Analyse The sanglifehrin-cyclophilin interaction: degradation work, synthetic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NMK
- Type
- protein
- Length
- 330 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-prolyl cis-trans isomerase a
- EC
- 5.2.1.8
- UniProt
- P62937
- Ligands
- SFM
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peptidyl-prolyl cis-trans isomerase a (EC 5.2.1.8) | protein | 165 | 14% helix, 34% strand | P62937 |
Ligands and binding sites
- SFM · (13E,15E)-(3S,6S,9R,10R,11S,12S,18S,21S)-10,12-dihydroxy-3-(3-hydroxyben-zyl)-18-((E)-3-hydroxy-1-methylpropenyl)-6-isopropyl-11-methyl-9-(3-oxo-butyl)-19-oxa-1,4,7,25-tetraaza-bicyclo[19.3.1]pentacosa-13,15-diene-2,5,8,20-tetraone · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 626 | 0.67 | 0.76 | 51 | SFM |
| 2 | 56 | 0.35 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 389 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1NMK · The Sanglifehrin-Cyclophilin Interaction: Degradation Work, Synthetic Macrocyclic… · the same entry in another collection · chain A against A, TM-score 1.00
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 P62937
- Elsewhere: RCSB PDB 1NMK · PDBe 1NMK · UniProt P62937
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