MolNFT v1 · #128605 · protein
Full length human cytoplasmic dynein-1 in the phi-particle conformation
5NVU · Dynein motor domain: “Full length human cytoplasmic dynein-1 in the phi-particle conformation”. Electron microscopy, 20 pockets (best druggability 0.84). MolNFT v1 #128605 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5NVU
- Type
- protein
- Length
- 10,378 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dynein motor domain; Dynein tail heavy chain; Dynein intermediate chain; Dynein light…
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 14 distinct chains · 59% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dynein motor domain | protein | 3169 | 56% helix, 9% strand | — |
| C | Dynein tail heavy chain | protein | 932 | 86% helix, 0% strand | — |
| D, E | Dynein intermediate chain | protein | 350 | 2% helix, 50% strand | — |
| F | Dynein tail heavy chain | protein | 893 | 86% helix, 0% strand | — |
| G | Dynein light intermediate chain | protein | 298 | 41% helix, 17% strand | — |
| H | Dynein light intermediate chain | protein | 295 | 39% helix, 15% strand | — |
| I | N-terminal dimerization domain | protein | 125 | 62% helix, 6% strand | — |
| J | N-terminal dimerization domain | protein | 124 | 65% helix, 8% strand | — |
| K, L | LC8 | protein | 85 | 36% helix, 45% strand | — |
| M | Tctex | protein | 103 | 36% helix, 36% strand | — |
| N | Tctex | protein | 104 | 36% helix, 38% strand | — |
| O | Intermediate chain N-terminus peptides | protein | 27 | 0% helix, 52% strand | — |
| P | Intermediate chain N-terminus peptides | protein | 29 | 0% helix, 45% strand | — |
| Q, R | Robl | protein | 120 | 45% helix, 29% 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 | 850 | 0.84 | 0.86 | 115 | empty |
| 2 | 793 | 0.84 | 0.87 | 112 | empty |
| 3 | 1035 | 0.83 | 0.85 | 104 | empty |
| 4 | 977 | 0.83 | 0.85 | 103 | empty |
| 5 | 1070 | 0.83 | 0.84 | 153 | empty |
Interfaces
23 interfaces between chains.
- M–N · 882 Ų buried · 20 hydrogen bonds · protein-protein
- C–E · 876 Ų buried · 35 hydrogen bonds · protein-protein
- K–L · 609 Ų buried · 15 hydrogen bonds · protein-protein
- I–J · 596 Ų buried · 6 hydrogen bonds · protein-protein
- Q–R · 563 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5NVU · Full length human cytoplasmic dynein-1 in the phi-particle conformation · 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
- Elsewhere: RCSB PDB 5NVU · PDBe 5NVU
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