MolNFT v1 · #170567 · protein
Scaffold-ligand complex with ligand unmodelled.
6YBM · Peptidyl-prolyl cis-trans isomerase F, mitochondrial: “Scaffold-ligand complex with ligand unmodelled.”. X-ray diffraction, 3 pockets (best druggability 0.82). MolNFT v1 #170567 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6YBM
- Type
- protein
- Length
- 492 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-prolyl cis-trans isomerase F, mitochondrial
- EC
- 5.2.1.8
- UniProt
- P30405
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Peptidyl-prolyl cis-trans isomerase F, mitochondrial (EC 5.2.1.8) | protein | 164 | 15% helix, 34% strand | P30405 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, C, B
- CIT · Citric acid · additive · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1163 | 0.82 | 0.83 | 112 | EDO, CIT |
| 2 | 166 | 0.46 | 0.76 | 26 | empty |
| 3 | 55 | 0.31 | 0.77 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 637 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 526 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 79 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6YBM · Scaffold-ligand complex with ligand unmodelled. · 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 P30405
- Elsewhere: RCSB PDB 6YBM · PDBe 6YBM · UniProt P30405
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