MolNFT v1 · #153344 · protein
Crystal structure of an actin monomer in complex with the nucleator cordon-bleu WH2-motif peptide mutant. T22V
6JBK · Actin, alpha skeletal muscle: “Crystal structure of an actin monomer in complex with the nucleator cordon-bleu WH2-motif peptide mutant. T22V”. X-ray diffraction, 2 ligands (ATP, CA), 9 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 6JBK
- Type
- protein
- Length
- 1,500 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle; Peptide from protein cordon-bleu
- UniProt
- P68135, Q5NBX1
- Ligands
- ATP, CA
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Actin, alpha skeletal muscle | protein | 353 | 46% helix, 19% strand | P68135 |
| B, D, F, H | Peptide from protein cordon-bleu | protein | 22 | 73% helix, 5% strand | Q5NBX1 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, C, E, G
- CA · Calcium ion · metal · 8 copies · chains A, G, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1027 | 0.85 | 0.85 | 77 | empty |
| 2 | 1156 | 0.82 | 0.82 | 76 | empty |
| 3 | 977 | 0.81 | 0.83 | 95 | ATP, CA |
| 4 | 1152 | 0.80 | 0.81 | 111 | ATP, CA |
| 5 | 331 | 0.77 | 0.88 | 46 | ATP, CA |
Interfaces
15 interfaces between chains.
- A–G · 992 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 959 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 936 Ų buried · 9 hydrogen bonds · protein-protein
- C–E · 924 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 915 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (methylation).
Compared structures
- 6JBK · Crystal structure of an actin monomer in complex with the nucleator Cordon-Bleu WH2-motif… · the same entry in another collection · chain G against G, TM-score 1.00
- P68135 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68135) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 Q5NBX1
- Elsewhere: RCSB PDB 6JBK · PDBe 6JBK · UniProt P68135 · UniProt Q5NBX1
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