MolNFT v1 · #127946 · protein
Crystal structure of the ARP4-N-actin-ARP8-INO80HSA module of INO80
5NBN · Actin-related protein 4: “Crystal structure of the ARP4-N-actin-ARP8-INO80HSA module of INO80”. X-ray diffraction, 3 ligands (ATP, LAR, CA), 20 pockets (best druggability 0.88). MolNFT v1 #127946 on GenesisL1: 3D structure, binding…
- PDB
- 5NBN
- Type
- protein
- Length
- 2,898 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin-related protein 4; Actin; Actin-like protein ARP8; Putative DNA helicase INO80
- EC
- 3.6.4.12
- UniProt
- P80428, P60010, Q12386, P53115
- Ligands
- ATP, LAR, CA
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Actin-related protein 4 | protein | 406 | 37% helix, 19% strand | P80428 |
| C, D | Actin | protein | 359 | 45% helix, 20% strand | P60010 |
| E, F | Actin-like protein ARP8 | protein | 598 | 42% helix, 15% strand | Q12386 |
| G, H | Putative DNA helicase INO80 (EC 3.6.4.12) | protein | 86 | 94% helix, 0% strand | P53115 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- LAR · Latrunculin A · ligand · 2 copies · chains C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1118 | 0.88 | 0.90 | 128 | CA, ATP |
| 2 | 656 | 0.88 | 0.93 | 104 | CA, ATP |
| 3 | 1168 | 0.86 | 0.87 | 111 | CA, ATP, LAR |
| 4 | 1197 | 0.86 | 0.87 | 115 | CA, ATP, LAR |
| 5 | 236 | 0.81 | 0.94 | 42 | empty |
Interfaces
11 interfaces between chains.
- C–E · 1498 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 1475 Ų buried · 15 hydrogen bonds · protein-protein
- E–G · 1102 Ų buried · 13 hydrogen bonds · protein-protein
- F–H · 1090 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1059 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 5NBN · Crystal structure of the Arp4-N-actin-Arp8-Ino80HSA module of INO80 · the same entry in another collection · chain H against H, TM-score 1.00
- P60010 · AlphaFold monomer V2.0 prediction for actin (P60010) · a predicted model of the same protein · chain C against A, TM-score 0.99
- Q12386 · AlphaFold monomer V2.0 prediction for actin-like protein ARP8 (Q12386) · a predicted model of the same protein · chain F against A, TM-score 0.99
- P80428 · AlphaFold monomer V2.0 prediction for actin-related protein 4 (P80428) · a predicted model of the same protein · chain B 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 P80428
- Every structure of UniProt P60010
- Every structure of UniProt Q12386
- Every structure of UniProt P53115
- Elsewhere: RCSB PDB 5NBN · PDBe 5NBN · UniProt P80428 · UniProt P60010 · UniProt Q12386 · UniProt P53115
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