MolNFT v1 · #153387 · protein
Crystal structure of an actin monomer in complex with a nucleator cordon-bleu WH2-motif peptide mutant. T22V, H11R
6JCU · Actin, alpha skeletal muscle: “Crystal structure of an actin monomer in complex with a nucleator cordon-bleu WH2-motif peptide mutant. T22V…”. X-ray diffraction, 2 ligands (ATP, CA), 6 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 6JCU
- Type
- protein
- Length
- 765 residues
- Chains
- 4
- 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
- 6 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Actin, alpha skeletal muscle | protein | 361 | 46% helix, 21% strand | P68135 |
| B, D | Peptide from protein cordon-bleu | protein | 22 | 68% helix, 5% strand | Q5NBX1 |
| C | Actin, alpha skeletal muscle | protein | 360 | 46% helix, 21% strand | P68135 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, C
- CA · Calcium ion · metal · 3 copies · chains A, C
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 | 1058 | 0.84 | 0.85 | 108 | ATP, CA |
| 2 | 394 | 0.72 | 0.83 | 52 | ATP, CA |
| 3 | 267 | 0.55 | 0.77 | 33 | empty |
| 4 | 143 | 0.53 | 0.80 | 29 | empty |
| 5 | 72 | 0.38 | 0.78 | 15 | CA |
Interfaces
3 interfaces between chains.
- C–D · 998 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 939 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 892 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 6JCU · Crystal structure of an actin monomer in complex with a nucleator Cordon-Bleu WH2-motif… · the same entry in another collection · chain D against D, 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
- Q5NBX1 · AlphaFold monomer V2.0 prediction for protein cordon-bleu (Q5NBX1) · a predicted model of the same protein · chain B against A, TM-score 0.48
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 6JCU · PDBe 6JCU · UniProt P68135 · UniProt Q5NBX1
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