MolNFT v1 · #68105 · protein
Electron cryo-microscopy of dngr-1 in complex with F-actin
3J82 · C-type lectin domain family 9 member a: “Electron cryo-microscopy of dngr-1 in complex with F-actin”. Electron microscopy, 2 ligands (ADP, CA), 12 pockets (best druggability 0.83). MolNFT v1 #68105 on GenesisL1: 3D structure…
- PDB
- 3J82
- Type
- protein
- Length
- 1,253 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-type lectin domain family 9 member a; Actin, cytoplasmic 1
- UniProt
- Q8BRU4, P60709
- Ligands
- ADP, CA
- Pockets
- 12 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C-type lectin domain family 9 member a | protein | 131 | 18% helix, 27% strand | Q8BRU4 |
| B, C, D | Actin, cytoplasmic 1 | protein | 374 | 42% helix, 16% strand | P60709 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains B, C, D
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.83 | 0.84 | 111 | ADP |
| 2 | 772 | 0.81 | 0.85 | 89 | ADP |
| 3 | 709 | 0.81 | 0.85 | 82 | ADP |
| 4 | 750 | 0.77 | 0.81 | 65 | empty |
| 5 | 304 | 0.68 | 0.82 | 45 | empty |
Interfaces
6 interfaces between chains.
- C–D · 816 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 427 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 360 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 305 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 301 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 modified (methylation).
Compared structures
- 3J82 · Electron cryo-microscopy of DNGR-1 in complex with F-actin · the same entry in another collection · chain D against D, TM-score 1.00
- P60709 · AlphaFold monomer V2.0 prediction for actin, cytoplasmic 1 (P60709) · a predicted model of the same protein · chain C against A, TM-score 0.93
- Q8BRU4 · AlphaFold monomer V2.0 prediction for C-type lectin domain family 9 member a (Q8BRU4) · a predicted model of the same protein · chain A against A, TM-score 0.89
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 Q8BRU4
- Every structure of UniProt P60709
- Elsewhere: RCSB PDB 3J82 · PDBe 3J82 · UniProt Q8BRU4 · UniProt P60709
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