Research workbench
The pointed end complex of dynactin bound to BICDR1
Analyse The pointed end complex of dynactin bound to BICDR1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Z8M
- Type
- protein
- Length
- 2,272 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dynactin subunit 2; Bicd family-like cargo adapter 1; Dynactin 6; Dynactin subunit 4…
- UniProt
- A0A4X1W6J2, A0JNT9, D0G6S1, A0A4X1TB62, I3LHK5, F2Z5G5, Q6QAQ1, A0A286ZK88
- Ligands
- ADP, ATP, MG, ZN
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 9 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M | Dynactin subunit 2 | protein | 24 | 13% helix, 13% strand | A0A4X1W6J2 |
| X | Bicd family-like cargo adapter 1 | protein | 15 | 73% helix, 0% strand | A0JNT9 |
| U | Dynactin 6 | protein | 178 | 8% helix, 25% strand | D0G6S1 |
| Y | Dynactin subunit 4 | protein | 383 | 19% helix, 28% strand | A0A4X1TB62 |
| J | ARP11 | protein | 379 | 41% helix, 18% strand | I3LHK5 |
| G | ARP1 actin related protein 1 homolog a | protein | 369 | 41% helix, 20% strand | F2Z5G5 |
| H | Actin, cytoplasmic 1 | protein | 372 | 45% helix, 20% strand | Q6QAQ1 |
| V | Dynactin subunit 5 | protein | 182 | 9% helix, 35% strand | A0A286ZK88 |
| I | ARP1 actin related protein 1 homolog a | protein | 370 | 42% helix, 20% strand | F2Z5G5 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains G, H, I
- ATP · Adenosine-5'-triphosphate · ligand · chains Y, J
- MG · Magnesium ion · metal · 4 copies · chains J, G, H, I
- 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1153 | 0.81 | 0.82 | 84 | empty |
| 2 | 720 | 0.80 | 0.84 | 78 | ATP, MG |
| 3 | 624 | 0.79 | 0.84 | 74 | empty |
| 4 | 955 | 0.76 | 0.79 | 67 | empty |
| 5 | 467 | 0.76 | 0.84 | 63 | ADP, MG |
Interfaces
14 interfaces between chains.
- Y–J · 3059 Ų buried · 25 hydrogen bonds · protein-protein
- Y–V · 1681 Ų buried · 8 hydrogen bonds · protein-protein
- J–I · 1285 Ų buried · 18 hydrogen bonds · protein-protein
- J–H · 1174 Ų buried · 10 hydrogen bonds · protein-protein
- G–I · 1145 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7Z8M · The pointed end complex of dynactin bound to BICDR1 · the same entry in another collection · chain I against I, TM-score 1.00
- Q6QAQ1 · AlphaFold monomer V2.0 prediction for actin, cytoplasmic 1 (Q6QAQ1) · a predicted model of the same protein · chain H against A, TM-score 0.96
- A0JNT9 · AlphaFold monomer V2.0 prediction for bicd family-like cargo adapter 1 (A0JNT9) · a predicted model of the same protein · chain X against A, TM-score 0.77
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 A0A4X1W6J2
- Every structure of UniProt A0JNT9
- Every structure of UniProt D0G6S1
- Every structure of UniProt A0A4X1TB62
- Every structure of UniProt I3LHK5
- Every structure of UniProt F2Z5G5
- Every structure of UniProt Q6QAQ1
- Every structure of UniProt A0A286ZK88
- Elsewhere: RCSB PDB 7Z8M · PDBe 7Z8M · UniProt A0A4X1W6J2 · UniProt A0JNT9 · UniProt D0G6S1 · UniProt A0A4X1TB62 · UniProt I3LHK5 · UniProt F2Z5G5 · UniProt Q6QAQ1 · UniProt A0A286ZK88
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