Research workbench
N terminal region of dynein tail domains in complex with dynactin filament and bicdr-1
Analyse N terminal region of dynein tail domains in complex with dynactin filament and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F1U
- Type
- protein
- Length
- 3,555 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ARP1 actin related protein 1 homolog a; Capping protein (actin filament) muscle Z-line…
- UniProt
- F2Z5G5, A0PFK5, A9XFX6, F1SKF9, F1SL58, Q14204, Q13409, A0JNT9
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 11 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D, F | ARP1 actin related protein 1 homolog a | protein | 370 | 36% helix, 18% strand | F2Z5G5 |
| 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 |
| c | Dynactin subunit 2 | protein | 37 | 16% helix, 16% strand | F1SKF9 |
| d | Dynactin subunit 2 | protein | 24 | 13% helix, 13% strand | F1SL58 |
| f | Cytoplasmic dynein 1 heavy chain 1 | protein | 596 | 70% helix, 1% strand | Q14204 |
| m | Cytoplasmic dynein 1 heavy chain 1 | protein | 396 | 73% helix, 0% strand | Q14204 |
| n | Cytoplasmic dynein 1 heavy chain 1 | protein | 341 | 73% helix, 0% strand | Q14204 |
| h | Cytoplasmic dynein 1 intermediate chain 2 | protein | 358 | 4% helix, 30% strand | Q13409 |
| X | Bicd family-like cargo adapter 1 | protein | 79 | 97% helix, 0% strand | A0JNT9 |
| x | Bicd family-like cargo adapter 1 | protein | 67 | 97% helix, 0% strand | A0JNT9 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains B, D, F
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 | 998 | 0.79 | 0.81 | 99 | empty |
| 2 | 469 | 0.74 | 0.84 | 45 | empty |
| 3 | 403 | 0.74 | 0.84 | 64 | ADP |
| 4 | 1172 | 0.72 | 0.76 | 75 | empty |
| 5 | 407 | 0.72 | 0.83 | 67 | ADP |
Interfaces
24 interfaces between chains.
- K–L · 3802 Ų buried · 53 hydrogen bonds · protein-protein
- X–x · 1863 Ų buried · 16 hydrogen bonds · protein-protein
- f–h · 1667 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1113 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 1112 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6F1U · N terminal region of dynein tail domains in complex with dynactin filament and BICDR-1 · the same entry in another collection · chain x against x, 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 A0PFK5
- Every structure of UniProt A9XFX6
- Every structure of UniProt F1SKF9
- Every structure of UniProt F1SL58
- Every structure of UniProt Q14204
- Every structure of UniProt Q13409
- Every structure of UniProt A0JNT9
- Elsewhere: RCSB PDB 6F1U · PDBe 6F1U · UniProt F2Z5G5 · UniProt A0PFK5 · UniProt A9XFX6 · UniProt F1SKF9 · UniProt F1SL58 · UniProt Q14204 · UniProt Q13409 · UniProt A0JNT9
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