Research workbench
Crystal structure of the ARP4-N-ACTIN(APO-state) heterodimer bound by a nanobody
Analyse Crystal structure of the ARP4-N-ACTIN(APO-state) heterodimer bound by a nanobody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NBL
- Type
- protein
- Length
- 1,810 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin-related protein 4; Actin; Nact-nanobody; Unknown peptide
- UniProt
- P80428, P60010
- Ligands
- ATP, CA
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 6 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Actin-related protein 4 | protein | 397 | 38% helix, 20% strand | P80428 |
| C, D | Actin | protein | 366 | 45% helix, 19% strand | P60010 |
| E | Nact-nanobody | protein | 122 | 7% helix, 50% strand | — |
| F | Nact-nanobody | protein | 124 | 7% helix, 52% strand | — |
| G | Unknown peptide | protein | 18 | 89% helix, 0% strand | — |
| H | Unknown peptide | protein | 20 | 90% helix, 0% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1001 | 0.88 | 0.90 | 106 | CA, ATP |
| 2 | 754 | 0.86 | 0.89 | 126 | empty |
| 3 | 474 | 0.83 | 0.90 | 54 | empty |
| 4 | 371 | 0.83 | 0.92 | 54 | empty |
| 5 | 243 | 0.82 | 0.94 | 40 | CA, ATP |
Interfaces
16 interfaces between chains.
- D–F · 1079 Ų buried · 23 hydrogen bonds · protein-protein
- C–E · 1071 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 1052 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1032 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 741 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, methylation).
Compared structures
- 5NBL · Crystal structure of the Arp4-N-actin(APO-state) heterodimer bound by a nanobody · the same entry in another collection · chain H against H, TM-score 1.00
- P80428 · AlphaFold monomer V2.0 prediction for actin-related protein 4 (P80428) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P60010 · AlphaFold monomer V2.0 prediction for actin (P60010) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P80428
- Every structure of UniProt P60010
- Elsewhere: RCSB PDB 5NBL · PDBe 5NBL · UniProt P80428 · UniProt P60010
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