Research workbench
Crystal structure of plasmepsin IV
Analyse Crystal structure of plasmepsin IV in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I70
- Type
- protein
- Length
- 646 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasmepsin IV; Pepstatin a
- UniProt
- W7FF86
- Ligands
- IVA
- Pockets
- 2 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Plasmepsin IV | protein | 321 | 14% helix, 47% strand | W7FF86 |
| A | Plasmepsin IV | protein | 315 | 13% helix, 47% strand | W7FF86 |
| C, D | Pepstatin a | protein | 5 | 0% helix, 20% strand | — |
Ligands and binding sites
- IVA · Isovaleric acid · ligand · 2 copies · chains B, A, C, D
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 | 1092 | 0.83 | 0.84 | 104 | IVA |
| 2 | 67 | 0.48 | 0.83 | 14 | empty |
Interfaces
5 interfaces between chains.
- B–A · 1028 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 613 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 609 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 96 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 14 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 modified, 2 covalent (disulfide, nonstandard, covalent ligand).
Compared structures
- 5I70 · Crystal Structure of plasmepsin IV · the same entry in another collection · chain B against B, 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 W7FF86
- Elsewhere: RCSB PDB 5I70 · PDBe 5I70 · UniProt W7FF86
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