Research workbench
Crystal structure of the FK506 binding domain of plasmodium vivax FKBP35 in complex with a tetrapeptide substrate
Analyse Crystal structure of the FK506 binding domain of plasmodium vivax FKBP35 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ITZ
- Type
- protein
- Length
- 246 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 70 kda peptidylprolyl isomerase; Substrate peptide
- EC
- 5.2.1.8
- UniProt
- A5K8X6
- Ligands
- NIT, SO4
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 70 kda peptidylprolyl isomerase (EC 5.2.1.8) | protein | 121 | 12% helix, 39% strand | A5K8X6 |
| C | Substrate peptide | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- NIT · 4-nitroaniline · ligand · chains A, B, C
- SO4 · Sulfate ion · ion · chains B
- SIN · Succinic acid · additive · chains A, C
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 | 175 | 0.59 | 0.82 | 29 | SIN |
| 2 | 163 | 0.47 | 0.76 | 32 | NIT |
Interfaces
3 interfaces between chains.
- A–B · 773 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 331 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 175 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 disulfide (additive adduct, covalent ligand, disulfide).
Compared structures
- 4ITZ · Crystal structure of the FK506 binding domain of Plasmodium vivax FKBP35 in complex with… · 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 A5K8X6
- Elsewhere: RCSB PDB 4ITZ · PDBe 4ITZ · UniProt A5K8X6
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