MolNFT v1 · #16018 · protein
Crystal structure of D. discoideum actin-gelsolin segment 1 complex crystallized in presence of lithium ATP
1NMD: “Crystal structure of D. discoideum actin-gelsolin segment 1 complex crystallized in presence of lithium ATP”. X-ray diffraction, 4 ligands (ATP, SO2, CA), 4 pockets (best druggability 0.74). MolNFT v1 #16018 on GenesisL1: 3D…
- PDB
- 1NMD
- Type
- protein
- Length
- 485 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin; Gelsolin
- UniProt
- P02577, P06396
- Ligands
- ATP, SO2, CA, SO4
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Actin | protein | 362 | 44% helix, 20% strand | P02577 |
| G | Gelsolin | protein | 123 | 24% helix, 35% strand | P06396 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- SO2 · Sulfur dioxide · ligand · chains A
- CA · Calcium ion · metal · chains G
- SO4 · Sulfate ion · ion · chains A
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 | 482 | 0.74 | 0.83 | 49 | ATP |
| 2 | 202 | 0.65 | 0.84 | 31 | empty |
| 3 | 155 | 0.43 | 0.75 | 21 | empty |
| 4 | 76 | 0.30 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–G · 997 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1NMD · Crystal Structure of D. Discoideum Actin-Gelsolin Segment 1 Complex Crystallized In… · the same entry in another collection · chain A against A, TM-score 1.00
- P06396 · AlphaFold monomer V2.0 prediction for gelsolin (P06396) · 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 P02577
- Every structure of UniProt P06396
- Elsewhere: RCSB PDB 1NMD · PDBe 1NMD · UniProt P02577 · UniProt P06396
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