MolNFT v1 · #14578 · protein
Crystal structure of the chicken actin trimer complexed with human gelsolin segment 1 (gs-1)
1MDU · Gelsolin precursor: “Crystal structure of the chicken actin trimer complexed with human gelsolin segment 1 (gs-1)”. X-ray diffraction, 2 ligands (ATP, CA), 10 pockets (best druggability 0.77). MolNFT v1 #14578 on GenesisL1: 3D…
- PDB
- 1MDU
- Type
- protein
- Length
- 970 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gelsolin precursor; A-actin
- UniProt
- P06396, P68139
- Ligands
- ATP, CA
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gelsolin precursor | protein | 124 | 23% helix, 34% strand | P06396 |
| B | A-actin | protein | 361 | 44% helix, 20% strand | P68139 |
| D | Gelsolin precursor | protein | 123 | 24% helix, 33% strand | P06396 |
| E | A-actin | protein | 362 | 43% helix, 20% strand | P68139 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains B, E
- CA · Calcium ion · metal · 7 copies · chains A, B, D, E
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 454 | 0.77 | 0.85 | 54 | CA, ATP |
| 2 | 381 | 0.75 | 0.86 | 51 | CA, ATP |
| 3 | 427 | 0.65 | 0.78 | 44 | TRS |
| 4 | 296 | 0.61 | 0.78 | 34 | empty |
| 5 | 333 | 0.61 | 0.77 | 36 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1044 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1036 Ų buried · 20 hydrogen bonds · protein-protein
- A–E · 702 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 1MDU · Crystal structure of the chicken actin trimer complexed with human gelsolin segment 1… · the same entry in another collection · chain E against E, TM-score 1.00
- P68139 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68139) · a predicted model of the same protein · chain E against A, TM-score 0.98
- P06396 · AlphaFold monomer V2.0 prediction for gelsolin (P06396) · a predicted model of the same protein · chain D 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 P06396
- Every structure of UniProt P68139
- Elsewhere: RCSB PDB 1MDU · PDBe 1MDU · UniProt P06396 · UniProt P68139
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