MolNFT v1 · #57372 · protein
Crystal structure of a dictyostelium P109I MG2+-actin in complex with human gelsolin segment 1
3A5M: “Crystal structure of a dictyostelium P109I MG2+-actin in complex with human gelsolin segment 1”. X-ray diffraction, 3 ligands (ATP, CA, MG), 4 pockets (best druggability 0.74). MolNFT v1 #57372 on GenesisL1: 3D structure, binding…
- PDB
- 3A5M
- Type
- protein
- Length
- 488 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gelsolin; Major actin
- UniProt
- P06396, P07830
- Ligands
- ATP, CA, MG
- 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 |
|---|---|---|---|---|---|
| S | Gelsolin | protein | 123 | 24% helix, 35% strand | P06396 |
| C | Major actin | protein | 365 | 44% helix, 20% strand | P07830 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains C
- CA · Calcium ion · metal · 2 copies · chains S, C
- MG · Magnesium ion · metal · chains C
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 | 465 | 0.74 | 0.83 | 59 | MG, ATP |
| 2 | 243 | 0.63 | 0.81 | 35 | empty |
| 3 | 185 | 0.49 | 0.76 | 21 | empty |
| 4 | 93 | 0.38 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- S–C · 1042 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 3A5M · Crystal Structure of a Dictyostelium P109I Mg2+-Actin in Complex with Human Gelsolin… · the same entry in another collection · chain S against S, TM-score 1.00
- P07830 · AlphaFold monomer V2.0 prediction for major actin (P07830) · a predicted model of the same protein · chain C against A, TM-score 0.97
- P06396 · AlphaFold monomer V2.0 prediction for gelsolin (P06396) · a predicted model of the same protein · chain S 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 P06396
- Every structure of UniProt P07830
- Elsewhere: RCSB PDB 3A5M · PDBe 3A5M · UniProt P06396 · UniProt P07830
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