Research workbench
Cryoem structure of dynactin complex at 4.0 ångström resolution
Analyse Cryoem structure of dynactin complex at 4.0 ångström resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ADX
- Type
- protein
- Length
- 7,306 residues
- Chains
- 27
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin related protein 1; Actin, cytoplasmic 1; Actin related protein 11; Capping protein…
- UniProt
- F2Z5G5, Q6QAQ1, I3LHK5, A0PFK5, D2JYW4, D0G6S1
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 17 distinct chains · 56% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, I | Actin related protein 1 | protein | 370 | 39% helix, 18% strand | F2Z5G5 |
| H | Actin, cytoplasmic 1 | protein | 370 | 43% helix, 16% strand | Q6QAQ1 |
| J | Actin related protein 11 | protein | 369 | 40% helix, 13% strand | I3LHK5 |
| K | Capping protein (actin filament) muscle Z-line, alpha 1 | protein | 275 | 38% helix, 31% strand | A0PFK5 |
| L | F-actin capping protein beta subunit variant II | protein | 270 | 42% helix, 31% strand | D2JYW4 |
| M | Dynactin subunit 2 | protein | 571 | 93% helix, 0% strand | — |
| N | Dynactin subunit 2 | protein | 602 | 90% helix, 0% strand | — |
| O, P | Dynactin subunit 3 | protein | 65 | 43% helix, 22% strand | — |
| Q, R | Dynactin subunit 2 | protein | 87 | 93% helix, 0% strand | — |
| U | Dynactin 5 | protein | 169 | 13% helix, 30% strand | D0G6S1 |
| V | Dynactin subunit 6 | protein | 165 | 11% helix, 25% strand | — |
| Y | Dynactin subunit 2 | protein | 243 | 10% helix, 12% strand | — |
| Z, z | Dynactin subunit 2 | protein | 419 | 93% helix, 0% strand | — |
| a | Dynactin subunit 2 | protein | 48 | 19% helix, 8% strand | — |
| b | Dynactin subunit 2 | protein | 71 | 13% helix, 8% strand | — |
| c | Dynactin subunit 2 | protein | 31 | 0% helix, 19% strand | — |
| d | Dynactin subunit 2 | protein | 20 | 0% helix, 15% strand | — |
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 | 700 | 0.84 | 0.88 | 91 | empty |
| 2 | 923 | 0.84 | 0.85 | 80 | empty |
| 3 | 739 | 0.83 | 0.86 | 82 | empty |
| 4 | 825 | 0.83 | 0.86 | 92 | empty |
| 5 | 1181 | 0.82 | 0.83 | 134 | empty |
Interfaces
65 interfaces between chains.
- Z–z · 4184 Ų buried · 0 hydrogen bonds · protein-protein
- K–L · 3885 Ų buried · 39 hydrogen bonds · protein-protein
- G–b · 1591 Ų buried · 15 hydrogen bonds · protein-protein
- J–Y · 1473 Ų buried · 11 hydrogen bonds · protein-protein
- I–J · 1379 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5ADX · CryoEM structure of dynactin complex at 4.0 angstrom resolution · the same entry in another collection · chain c against c, 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 D2JYW4
- Every structure of UniProt D0G6S1
- Elsewhere: RCSB PDB 5ADX · PDBe 5ADX · UniProt F2Z5G5 · UniProt Q6QAQ1 · UniProt I3LHK5 · UniProt A0PFK5 · UniProt D2JYW4 · UniProt D0G6S1
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