Research workbench
Ternary complex of ac-alpha-actin with profilin and CoA-NAA80
Analyse Ternary complex of ac-alpha-actin with profilin and CoA-NAA80 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NBE
- Type
- protein
- Length
- 694 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle; N-alpha-acetyltransferase 80; Profilin-1
- EC
- 2.3.1.-
- UniProt
- P68135, Q93015, P07737
- Ligands
- ATP, LAB, COA, CA
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Actin, alpha skeletal muscle | protein | 370 | 44% helix, 20% strand | P68135 |
| N | N-alpha-acetyltransferase 80 (EC 2.3.1.-) | protein | 186 | 28% helix, 26% strand | Q93015 |
| P | Profilin-1 | protein | 138 | 30% helix, 31% strand | P07737 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- LAB · Latrunculin B · ligand · chains A
- COA · Coenzyme A · ligand · chains A, N
- CA · Calcium ion · metal · chains A
- GOL · Glycerol · additive · 3 copies · chains A, N
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 741 | 0.77 | 0.81 | 67 | empty |
| 2 | 418 | 0.74 | 0.84 | 51 | CA, ATP, LAB |
| 3 | 204 | 0.60 | 0.81 | 29 | empty |
| 4 | 203 | 0.58 | 0.80 | 26 | empty |
| 5 | 153 | 0.50 | 0.78 | 23 | COA |
Interfaces
3 interfaces between chains.
- A–N · 1293 Ų buried · 21 hydrogen bonds · protein-protein
- A–P · 1159 Ų buried · 25 hydrogen bonds · protein-protein
- N–P · 449 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation, nonstandard).
Compared structures
- 6NBE · Ternary Complex of Ac-Alpha-Actin with Profilin and CoA-NAA80 · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.99
- P07737 · AlphaFold monomer V2.0 prediction for profilin-1 (P07737) · a predicted model of the same protein · chain P against A, TM-score 0.98
- Q93015 · AlphaFold monomer V2.0 prediction for N-alpha-acetyltransferase 80 (Q93015) · a predicted model of the same protein · chain N against A, TM-score 0.93
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 Q93015
- Every structure of UniProt P07737
- Elsewhere: RCSB PDB 6NBE · PDBe 6NBE · UniProt P68135 · UniProt Q93015 · UniProt P07737
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