Research workbench
Crystal structure of plasmodium falciparum actin I- gelsolin segment 1 -cdatp complex
Analyse Crystal structure of plasmodium falciparum actin I- gelsolin segment 1 -cdatp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MVV
- Type
- protein
- Length
- 475 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin-1; Gelsolin
- UniProt
- Q8I4X0, P13020
- Ligands
- ATP, CD, CA, SCN
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Actin-1 | protein | 350 | 44% helix, 21% strand | Q8I4X0 |
| G | Gelsolin | protein | 125 | 23% helix, 34% strand | P13020 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- CD · Cadmium ion · metal · 3 copies · chains A
- CA · Calcium ion · metal · 2 copies · chains A, G
- SCN · Thiocyanate ion · ion · chains A, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 342 | 0.73 | 0.85 | 48 | ATP, CD |
| 2 | 136 | 0.52 | 0.80 | 26 | empty |
| 3 | 134 | 0.43 | 0.76 | 17 | empty |
| 4 | 113 | 0.38 | 0.75 | 26 | SCN |
Interfaces
1 interface between chains.
- A–G · 1094 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5MVV · Crystal structure of Plasmodium falciparum actin I- gelsolin segment 1 -CdATP complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q8I4X0 · AlphaFold monomer V2.0 prediction for actin-1 (Q8I4X0) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P13020 · AlphaFold monomer V2.0 prediction for gelsolin (P13020) · a predicted model of the same protein · chain G against A, TM-score 0.95
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 Q8I4X0
- Every structure of UniProt P13020
- Elsewhere: RCSB PDB 5MVV · PDBe 5MVV · UniProt Q8I4X0 · UniProt P13020
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