MolNFT v1 · #171994 · protein
The pointed end complex of dynactin bound to BICDR1
6ZNM · ARP1 actin related protein 1 homolog a: “The pointed end complex of dynactin bound to BICDR1”. Electron microscopy, 3 ligands (ADP, ATP, ZN), 20 pockets (best druggability 0.83). MolNFT v1 #171994 on GenesisL1: 3D structure, binding…
- PDB
- 6ZNM
- Type
- protein
- Length
- 2,601 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, A0JNT9, A0A4X1TB62
- Ligands
- ADP, ATP, ZN
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 9 distinct chains · 37% helix, 17% 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 |
| X | Bicd family-like cargo adapter 1,BICD family-like cargo adapter 1,BICDR1 | protein | 139 | 98% helix, 0% strand | A0JNT9 |
| Y | Dynactin subunit 4 | protein | 410 | 14% helix, 21% strand | A0A4X1TB62 |
| x | Bicd family-like cargo adapter 1,BICD family-like cargo adapter 1,BICDR1 | protein | 142 | 97% helix, 0% strand | A0JNT9 |
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 | 935 | 0.83 | 0.85 | 88 | empty |
| 2 | 969 | 0.81 | 0.83 | 112 | ADP |
| 3 | 510 | 0.80 | 0.86 | 74 | empty |
| 4 | 202 | 0.76 | 0.92 | 37 | ATP |
| 5 | 302 | 0.76 | 0.88 | 31 | empty |
Interfaces
19 interfaces between chains.
- J–Y · 3113 Ų buried · 19 hydrogen bonds · protein-protein
- V–Y · 1756 Ų buried · 5 hydrogen bonds · protein-protein
- G–M · 1666 Ų buried · 20 hydrogen bonds · protein-protein
- I–J · 1338 Ų buried · 15 hydrogen bonds · protein-protein
- G–I · 1218 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6ZNM · The pointed end complex of dynactin bound to BICDR1 · the same entry in another collection · chain x against x, 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 0.59
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 A0JNT9
- Every structure of UniProt A0A4X1TB62
- Elsewhere: RCSB PDB 6ZNM · PDBe 6ZNM · UniProt F2Z5G5 · UniProt Q6QAQ1 · UniProt I3LHK5 · UniProt A0A5G2QD80 · UniProt D0G6S1 · UniProt A0A286ZK88 · UniProt A0JNT9 · UniProt A0A4X1TB62
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