Research workbench
Crystal structure of an actin dimer in complex with the actin nucleator cordon-bleu
Analyse Crystal structure of an actin dimer in complex with the actin nucleator… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JHD
- Type
- protein
- Length
- 1,640 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin-5C; Protein cordon-bleu
- UniProt
- P10987, Q5NBX1
- Ligands
- ANP, MG
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Actin-5C | protein | 371 | 41% helix, 19% strand | P10987 |
| B, E | Actin-5C | protein | 371 | 43% helix, 20% strand | P10987 |
| C | Protein cordon-bleu | protein | 81 | 35% helix, 1% strand | Q5NBX1 |
| F | Protein cordon-bleu | protein | 75 | 45% helix, 1% strand | Q5NBX1 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, C, B, D, F, E
- MG · Magnesium ion · metal · 4 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 524 | 0.77 | 0.85 | 75 | ANP, MG |
| 2 | 477 | 0.75 | 0.84 | 56 | ANP, MG |
| 3 | 831 | 0.74 | 0.78 | 88 | empty |
| 4 | 469 | 0.73 | 0.83 | 54 | ANP, MG |
| 5 | 497 | 0.73 | 0.82 | 54 | ANP, MG |
Interfaces
8 interfaces between chains.
- B–C · 2158 Ų buried · 24 hydrogen bonds · protein-protein
- D–F · 1915 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1837 Ų buried · 28 hydrogen bonds · protein-protein
- E–F · 1678 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 285 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4JHD · Crystal Structure of an Actin Dimer in Complex with the Actin Nucleator Cordon-Bleu · the same entry in another collection · chain F against F, TM-score 1.00
- P10987 · AlphaFold monomer V2.0 prediction for actin-5C (P10987) · a predicted model of the same protein · chain B against A, TM-score 0.96
- Q5NBX1 · AlphaFold monomer V2.0 prediction for protein cordon-bleu (Q5NBX1) · a predicted model of the same protein · chain F against A, TM-score 0.32
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 P10987
- Every structure of UniProt Q5NBX1
- Elsewhere: RCSB PDB 4JHD · PDBe 4JHD · UniProt P10987 · UniProt Q5NBX1
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