Research workbench
Actin dimer cross-linked by V. cholerae martx toxin and complexed with DNase I and gelsolin-segment 1
Analyse Actin dimer cross-linked by V. cholerae martx toxin and complexed with DNase I… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CJC
- Type
- protein
- Length
- 755 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle; Deoxyribonuclease-1; Gelsolin
- EC
- 3.1.21.1
- UniProt
- P68135, P00639, P06396
- Ligands
- ATP, NAG, CA, SO4
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Actin, alpha skeletal muscle | protein | 372 | 42% helix, 20% strand | P68135 |
| D | Deoxyribonuclease-1 (EC 3.1.21.1) | protein | 258 | 27% helix, 28% strand | P00639 |
| G | Gelsolin | protein | 125 | 25% helix, 31% strand | P06396 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains D
- CA · Calcium ion · metal · 2 copies · chains A, G
- SO4 · Sulfate ion · ion · 6 copies · chains A, D, 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 | 596 | 0.74 | 0.81 | 66 | CA, ATP |
| 2 | 401 | 0.68 | 0.80 | 41 | empty |
| 3 | 111 | 0.41 | 0.77 | 20 | empty |
| 4 | 104 | 0.35 | 0.74 | 21 | empty |
| 5 | 87 | 0.34 | 0.74 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–G · 1065 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 951 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3CJC · Actin dimer cross-linked by V. cholerae MARTX toxin and complexed with DNase I and… · the same entry in another collection · chain A against A, TM-score 1.00
- P00639 · AlphaFold monomer V2.0 prediction for deoxyribonuclease-1 (P00639) · a predicted model of the same protein · chain D against A, TM-score 0.99
- P68135 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68135) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P06396 · AlphaFold monomer V2.0 prediction for gelsolin (P06396) · a predicted model of the same protein · chain G against A, TM-score 0.94
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 P68135
- Every structure of UniProt P00639
- Every structure of UniProt P06396
- Elsewhere: RCSB PDB 3CJC · PDBe 3CJC · UniProt P68135 · UniProt P00639 · UniProt P06396
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.