Research workbench
The pointed end complex of dynactin with the P150 projection docked
Analyse The pointed end complex of dynactin with the P150 projection docked in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZNO
- Type
- protein
- Length
- 2,697 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ARP1 actin related protein 1 homolog a; Actin, cytoplasmic 1; ARP11; Dynactin subunit 2…
- UniProt
- F2Z5G5, Q6QAQ1, I3LHK5, A0A5G2QD80, D0G6S1, A0A286ZK88, A0A4X1TB62
- Ligands
- ADP, ATP, ZN
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 9 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, I | ARP1 actin related protein 1 homolog a | protein | 370 | 39% helix, 19% strand | F2Z5G5 |
| H | Actin, cytoplasmic 1 | protein | 370 | 41% helix, 19% strand | Q6QAQ1 |
| J | ARP11 | protein | 379 | 41% helix, 17% strand | I3LHK5 |
| M | Dynactin subunit 2 | protein | 75 | 17% helix, 8% strand | A0A5G2QD80 |
| U | Dynactin 6 | protein | 167 | 8% helix, 19% strand | D0G6S1 |
| V | Dynactin subunit 5 | protein | 179 | 8% helix, 30% strand | A0A286ZK88 |
| Y | Dynactin subunit 4 | protein | 410 | 14% helix, 21% strand | A0A4X1TB62 |
| Z | Dynactin subunit 1 | protein | 189 | 98% helix, 0% strand | — |
| z | Dynactin subunit 1 | protein | 188 | 98% helix, 0% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains G, I, J, Y
- ATP · Adenosine-5'-triphosphate · ligand · chains H
- ZN · Zinc ion · metal · 3 copies · chains Y
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 | 708 | 0.83 | 0.86 | 76 | empty |
| 2 | 456 | 0.83 | 0.90 | 61 | ADP |
| 3 | 588 | 0.81 | 0.86 | 79 | empty |
| 4 | 196 | 0.76 | 0.92 | 35 | ATP |
| 5 | 303 | 0.76 | 0.88 | 37 | empty |
Interfaces
17 interfaces between chains.
- J–Y · 3118 Ų buried · 19 hydrogen bonds · protein-protein
- Z–z · 2311 Ų buried · 0 hydrogen bonds · protein-protein
- V–Y · 1759 Ų buried · 5 hydrogen bonds · protein-protein
- G–M · 1668 Ų buried · 20 hydrogen bonds · protein-protein
- I–J · 1338 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
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 F2Z5G5
- Every structure of UniProt Q6QAQ1
- Every structure of UniProt I3LHK5
- Every structure of UniProt A0A5G2QD80
- Every structure of UniProt D0G6S1
- Every structure of UniProt A0A286ZK88
- Every structure of UniProt A0A4X1TB62
- Elsewhere: RCSB PDB 6ZNO · PDBe 6ZNO · UniProt F2Z5G5 · UniProt Q6QAQ1 · UniProt I3LHK5 · UniProt A0A5G2QD80 · UniProt D0G6S1 · UniProt A0A286ZK88 · UniProt A0A4X1TB62
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