Research workbench
Ternary complex of BETA/GAMMA-actin with profilin and ancoa-NAA80
Analyse Ternary complex of BETA/GAMMA-actin with profilin and ancoa-NAA80 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NBW
- Type
- protein
- Length
- 672 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, cytoplasmic 1; N-alpha-acetyltransferase 80; Profilin-1
- EC
- 2.3.1.-
- UniProt
- P60709, Q93015, P07737
- Ligands
- ATP, LAB, SOP, CA
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Actin, cytoplasmic 1 | protein | 367 | 45% helix, 20% strand | P60709 |
| N | N-alpha-acetyltransferase 80 (EC 2.3.1.-) | protein | 167 | 30% helix, 29% strand | Q93015 |
| P | Profilin-1 | protein | 138 | 29% helix, 32% strand | P07737 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- LAB · Latrunculin B · ligand · chains A
- SOP · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (3R)-3-hydroxy-2,2-dimethyl-4-oxo-4-{[3-oxo-3-({2-[(2-oxopropyl)thio]ethyl}amino)propyl]amino}butyl dihydrogen diphosphate · ligand · chains A, N
- CA · Calcium ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- 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
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.76 | 0.85 | 58 | CA, ATP, LAB |
| 2 | 589 | 0.70 | 0.79 | 74 | SOP |
| 3 | 206 | 0.59 | 0.81 | 32 | empty |
| 4 | 216 | 0.58 | 0.80 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–P · 1154 Ų buried · 22 hydrogen bonds · protein-protein
- A–N · 1073 Ų buried · 13 hydrogen bonds · protein-protein
- N–P · 451 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 6NBW · Ternary Complex of Beta/Gamma-Actin with Profilin and AnCoA-NAA80 · the same entry in another collection · chain A against A, TM-score 1.00
- P60709 · AlphaFold monomer V2.0 prediction for actin, cytoplasmic 1 (P60709) · 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 0.95
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 P60709
- Every structure of UniProt Q93015
- Every structure of UniProt P07737
- Elsewhere: RCSB PDB 6NBW · PDBe 6NBW · UniProt P60709 · UniProt Q93015 · UniProt P07737
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