Research workbench
Crystal structure of plasmodium berghei actin II in the mg-ADP state
Analyse Crystal structure of plasmodium berghei actin II in the mg-ADP state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I4M
- Type
- protein
- Length
- 485 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin-2; Gelsolin
- UniProt
- Q4YU79, P13020
- Ligands
- ADP, CA, MG, SCN
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Actin-2 | protein | 358 | 45% helix, 20% strand | Q4YU79 |
| G | Gelsolin | protein | 127 | 24% helix, 34% strand | P13020 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- CA · Calcium ion · metal · 2 copies · chains A, G
- MG · Magnesium ion · metal · chains A
- SCN · Thiocyanate ion · ion · 2 copies · chains A, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 327 | 0.75 | 0.87 | 50 | ADP, MG |
| 2 | 132 | 0.64 | 0.87 | 30 | empty |
| 3 | 98 | 0.41 | 0.77 | 16 | empty |
| 4 | 104 | 0.40 | 0.76 | 24 | SCN |
| 5 | 62 | 0.35 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–G · 1155 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 6I4M · Crystal Structure of Plasmodium berghei actin II in the Mg-ADP state · the same entry in another collection · chain G against G, TM-score 1.00
- Q4YU79 · AlphaFold monomer V2.0 prediction for actin-2 (Q4YU79) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P13020 · AlphaFold monomer V2.0 prediction for gelsolin (P13020) · a predicted model of the same protein · chain G against A, TM-score 0.92
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 Q4YU79
- Every structure of UniProt P13020
- Elsewhere: RCSB PDB 6I4M · PDBe 6I4M · UniProt Q4YU79 · UniProt P13020
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.