Research workbench
Cryo-EM structure of two dynein tail domains bound to dynactin and BICDR1
Analyse Cryo-EM structure of two dynein tail domains bound to dynactin and BICDR1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F1T
- Type
- protein
- Length
- 13,986 residues
- Chains
- 45
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ARP1 actin related protein 1 homolog a; Actin, cytoplasmic 1; Actin related protein 10…
- UniProt
- F2Z5G5, Q6QAQ1, I3LHK5, A0PFK5, A9XFX6, D0G6S1, A0A286ZK88, A0JNT9, F1SKF9, Q14204, Q13409, O43237, Q9NP97
- Ligands
- ADP, ATP
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 29 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, I | ARP1 actin related protein 1 homolog a | protein | 370 | 35% helix, 20% strand | F2Z5G5 |
| H | Actin, cytoplasmic 1 | protein | 370 | 41% helix, 18% strand | Q6QAQ1 |
| J | Actin related protein 10 homolog | protein | 369 | 40% helix, 13% strand | I3LHK5 |
| K | Capping protein (actin filament) muscle Z-line, alpha 1 | protein | 278 | 40% helix, 25% strand | A0PFK5 |
| L | F-actin capping protein beta subunit | protein | 269 | 38% helix, 26% strand | A9XFX6 |
| M | Dynactin subunit 2 | protein | 587 | 93% helix, 0% strand | — |
| N | Dynactin subunit 2 | protein | 616 | 90% helix, 0% strand | — |
| O, P | Dynactin subunit 3 | protein | 65 | 43% helix, 28% strand | — |
| Q, R | Dynactin subunit 2 | protein | 87 | 89% helix, 0% strand | — |
| U | Dynactin 6 | protein | 171 | 13% helix, 14% strand | D0G6S1 |
| V | Dynactin subunit 5 | protein | 165 | 8% helix, 16% strand | A0A286ZK88 |
| X | Bicd family-like cargo adapter 1,BICD family-like cargo adapter 1,BICD family-like cargo adapter 1,BICDR-1 | protein | 285 | 99% helix, 0% strand | A0JNT9 |
| Y | Dynactin subunit 4 | protein | 263 | 11% helix, 6% strand | — |
| Z | Dynactin subunit 1 | protein | 52 | 67% helix, 0% strand | — |
| a | Dynactin subunit 2 | protein | 52 | 21% helix, 12% strand | F1SKF9 |
| b | Dynactin subunit 2 | protein | 75 | 9% helix, 5% strand | F1SKF9 |
| c | Dynactin subunit 2 | protein | 37 | 16% helix, 16% strand | F1SKF9 |
| d | Dynactin subunit 2 | protein | 24 | 13% helix, 13% strand | F1SKF9 |
| e, m | Cytoplasmic dynein 1 heavy chain 1,CYTOPLASMIC dynein 1 heavy chain 1,CYTOPLASMIC dynein 1 heavy chain 1,DYNEIN heavy chain, cytoplasmic dynein 1 heavy chain 1,CYTOPLASMIC dynein 1 heavy chain 1,CYTOPLASMIC dynein 1 heavy chain 1,CYTOPLASMIC dynein 1 heavy chain 1,DYNEIN heavy CHAIN,CYTOPLASMIC dynein 1 heavy chain 1,CYTOPLASMIC dynein 1 heavy chain 1 | protein | 926 | 67% helix, 2% strand | Q14204 |
| f | Cytoplasmic dynein 1 heavy chain 1,CYTOPLASMIC dynein 1 heavy chain 1,CYTOPLASMIC dynein 1 heavy chain 1,DYNEIN heavy chain, cytoplasmic dynein 1 heavy chain 1,CYTOPLASMIC dynein 1 heavy chain 1,CYTOPLASMIC dynein 1 heavy chain 1,CYTOPLASMIC dynein 1 heavy chain 1,DYNEIN heavy CHAIN,CYTOPLASMIC dynein 1 heavy chain 1,CYTOPLASMIC dynein 1 heavy chain 1 | protein | 929 | 66% helix, 4% strand | Q14204 |
| g, o | Cytoplasmic dynein 1 intermediate chain 2 | protein | 397 | 10% helix, 28% strand | Q13409 |
| h | Cytoplasmic dynein 1 intermediate chain 2 | protein | 400 | 8% helix, 27% strand | Q13409 |
| i, q, r | Cytoplasmic dynein 1 light intermediate chain 2 | protein | 268 | 41% helix, 11% strand | O43237 |
| j | Cytoplasmic dynein 1 light intermediate chain 2 | protein | 288 | 35% helix, 11% strand | O43237 |
| k, l, s, t | Dynein light chain roadblock-type 1 | protein | 93 | 35% helix, 16% strand | Q9NP97 |
| n | Cytoplasmic dynein 1 heavy chain 1,CYTOPLASMIC dynein 1 heavy chain 1,CYTOPLASMIC dynein 1 heavy chain 1,DYNEIN heavy chain, cytoplasmic dynein 1 heavy chain 1,CYTOPLASMIC dynein 1 heavy chain 1,CYTOPLASMIC dynein 1 heavy chain 1,CYTOPLASMIC dynein 1 heavy chain 1,DYNEIN heavy CHAIN,CYTOPLASMIC dynein 1 heavy chain 1,CYTOPLASMIC dynein 1 heavy chain 1 | protein | 928 | 67% helix, 4% strand | Q14204 |
| p | Cytoplasmic dynein 1 intermediate chain 2 | protein | 401 | 9% helix, 25% strand | Q13409 |
| x | Bicd family-like cargo adapter 1,BICD family-like cargo adapter 1,BICD family-like cargo adapter 1 | protein | 288 | 99% helix, 0% strand | A0JNT9 |
| z | Dynactin subunit 1 | protein | 53 | 72% helix, 0% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 9 copies · chains A, B, C, a, D, E, F, G, I, J
- ATP · Adenosine-5'-triphosphate · ligand · chains H
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 | 992 | 0.87 | 0.88 | 105 | empty |
| 2 | 928 | 0.85 | 0.86 | 107 | ADP |
| 3 | 891 | 0.85 | 0.87 | 90 | empty |
| 4 | 2074 | 0.85 | 0.86 | 248 | empty |
| 5 | 2111 | 0.84 | 0.85 | 198 | empty |
Interfaces
105 interfaces between chains.
- K–L · 3802 Ų buried · 53 hydrogen bonds · protein-protein
- X–x · 3557 Ų buried · 16 hydrogen bonds · protein-protein
- f–h · 1841 Ų buried · 23 hydrogen bonds · protein-protein
- G–b · 1614 Ų buried · 11 hydrogen bonds · protein-protein
- m–o · 1557 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 6F1T · Cryo-EM structure of two dynein tail domains bound to dynactin and BICDR1 · the same entry in another collection · chain K against K, TM-score 1.00
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 A0PFK5
- Every structure of UniProt A9XFX6
- Every structure of UniProt D0G6S1
- Every structure of UniProt A0A286ZK88
- Every structure of UniProt A0JNT9
- Every structure of UniProt F1SKF9
- Every structure of UniProt Q14204
- Every structure of UniProt Q13409
- Every structure of UniProt O43237
- Every structure of UniProt Q9NP97
- Elsewhere: RCSB PDB 6F1T · PDBe 6F1T · UniProt F2Z5G5 · UniProt Q6QAQ1 · UniProt I3LHK5 · UniProt A0PFK5 · UniProt A9XFX6 · UniProt D0G6S1 · UniProt A0A286ZK88 · UniProt A0JNT9 · UniProt F1SKF9 · UniProt Q14204 · UniProt Q13409 · UniProt O43237 · UniProt Q9NP97
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