Research workbench
Mucor circinelloides FKBP12 protein bound with FK506 in P3221 space group
Analyse Mucor circinelloides FKBP12 protein bound with FK506 in P3221 space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VRX
- Type
- protein
- Length
- 429 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidylprolyl isomerase
- EC
- 5.2.1.8
- UniProt
- U3N5X4
- Ligands
- FK5
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Peptidylprolyl isomerase (EC 5.2.1.8) | protein | 108 | 9% helix, 40% strand | U3N5X4 |
| B | Peptidylprolyl isomerase (EC 5.2.1.8) | protein | 107 | 11% helix, 40% strand | U3N5X4 |
| D | Peptidylprolyl isomerase (EC 5.2.1.8) | protein | 106 | 11% helix, 39% strand | U3N5X4 |
Ligands and binding sites
- FK5 · 8-deethyl-8-[but-3-enyl]-ascomycin · ligand · 4 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 903 | 0.74 | 0.78 | 68 | empty |
| 2 | 86 | 0.46 | 0.80 | 14 | FK5 |
| 3 | 101 | 0.42 | 0.76 | 12 | empty |
| 4 | 98 | 0.42 | 0.76 | 14 | empty |
| 5 | 82 | 0.40 | 0.77 | 13 | empty |
Interfaces
6 interfaces between chains.
- B–D · 483 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 445 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 267 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 245 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 213 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6VRX · Mucor circinelloides FKBP12 protein bound with FK506 in P3221 space group · 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 U3N5X4
- Elsewhere: RCSB PDB 6VRX · PDBe 6VRX · UniProt U3N5X4
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