MolNFT v1 · #128615 · protein
Human cytoplasmic dynein-1 bound to dynactin and an N-terminal construct of BICD2
5NW4 · Dynein heavy chain: “Human cytoplasmic dynein-1 bound to dynactin and an N-terminal construct of BICD2”. Electron microscopy, 20 pockets (best druggability 0.84). MolNFT v1 #128615 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5NW4
- Type
- protein
- Length
- 10,707 residues
- Chains
- 39
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dynein heavy chain; Dynein intermediate chain; Dynein N-terminal dimerization domain…
- UniProt
- F2Z5G5, I3LVD5, I3LHK5, A0PFK5, D2JYW4, D0G6S1, A0A0J9X292, A0A0J9X293, A0A0J9X299
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 28 distinct chains · 57% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Dynein heavy chain | protein | 889 | 86% helix, 0% strand | — |
| D | Dynein intermediate chain | protein | 341 | 2% helix, 51% strand | — |
| C | Dynein intermediate chain | protein | 350 | 2% helix, 51% strand | — |
| A | Dynein heavy chain | protein | 922 | 86% helix, 0% strand | — |
| 1 | Dynein N-terminal dimerization domain | protein | 125 | 62% helix, 6% strand | — |
| 2 | Dynein N-terminal dimerization domain | protein | 124 | 65% helix, 8% strand | — |
| R, S | Robl | protein | 120 | 45% helix, 29% strand | — |
| E | Dynein light intermediate chain | protein | 295 | 39% helix, 15% strand | — |
| F | Dynein light intermediate chain | protein | 298 | 41% helix, 17% strand | — |
| G, H, O, P, Q, T, U, W | ARP1 | protein | 370 | 39% helix, 18% strand | F2Z5G5 |
| V | Beta-actin | protein | 370 | 43% helix, 16% strand | I3LVD5 |
| X | ARP11 | protein | 369 | 40% helix, 13% strand | I3LHK5 |
| Y | Capping protein (actin filament) muscle Z-line, alpha 1 | protein | 275 | 38% helix, 31% strand | A0PFK5 |
| Z | F-actin capping protein beta subunit variant II | protein | 270 | 42% helix, 31% strand | D2JYW4 |
| a | Dynactin shoulder complex | protein | 571 | 93% helix, 0% strand | — |
| b | Dynactin shoulder complex | protein | 602 | 90% helix, 0% strand | — |
| c, d | Dynactin shoulder complex | protein | 65 | 43% helix, 22% strand | — |
| e, f | Dynactin shoulder complex | protein | 87 | 93% helix, 0% strand | — |
| g | Dynactin 6 | protein | 169 | 13% helix, 30% strand | D0G6S1 |
| h | Dynactin subunit 5 | protein | 165 | 11% helix, 25% strand | — |
| i | Dynactin pointed end P62 | protein | 243 | 10% helix, 12% strand | — |
| j | P150 | protein | 52 | 67% helix, 0% strand | — |
| k | Dynactin | protein | 48 | 19% helix, 8% strand | A0A0J9X292 |
| l | Dynactin | protein | 71 | 13% helix, 8% strand | A0A0J9X293 |
| m | Dynactin | protein | 31 | 0% helix, 19% strand | A0A0J9X299 |
| n | Dynactin | protein | 20 | 0% helix, 15% strand | — |
| o | Dynactin P150 | protein | 53 | 75% helix, 0% strand | — |
| 5, 6 | BICD2N | protein | 275 | 99% helix, 0% 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 | 964 | 0.84 | 0.85 | 100 | empty |
| 2 | 574 | 0.83 | 0.88 | 75 | empty |
| 3 | 746 | 0.83 | 0.86 | 98 | empty |
| 4 | 809 | 0.83 | 0.86 | 90 | empty |
| 5 | 1136 | 0.82 | 0.84 | 85 | empty |
Interfaces
76 interfaces between chains.
- Y–Z · 3889 Ų buried · 39 hydrogen bonds · protein-protein
- 5–6 · 2410 Ų buried · 0 hydrogen bonds · protein-protein
- U–l · 1592 Ų buried · 15 hydrogen bonds · protein-protein
- X–i · 1473 Ų buried · 11 hydrogen bonds · protein-protein
- W–X · 1382 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5NW4 · Human cytoplasmic dynein-1 bound to dynactin and an N-terminal construct of BICD2 · the same entry in another collection · chain D against D, 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 I3LVD5
- Every structure of UniProt I3LHK5
- Every structure of UniProt A0PFK5
- Every structure of UniProt D2JYW4
- Every structure of UniProt D0G6S1
- Every structure of UniProt A0A0J9X292
- Every structure of UniProt A0A0J9X293
- Every structure of UniProt A0A0J9X299
- Elsewhere: RCSB PDB 5NW4 · PDBe 5NW4 · UniProt F2Z5G5 · UniProt I3LVD5 · UniProt I3LHK5 · UniProt A0PFK5 · UniProt D2JYW4 · UniProt D0G6S1 · UniProt A0A0J9X292 · UniProt A0A0J9X293 · UniProt A0A0J9X299
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