Research workbench
Structure of the dynein-2 complex; ift-train bound model
Analyse Structure of the dynein-2 complex; ift-train bound model in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SC2
- Type
- protein
- Length
- 10,108 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O6-alkylguanine-DNA alkyltransferase MUTANT,DYNC2H1 variant PROTEIN,O6-alkylguanine-DNA…
- UniProt
- E5BBQ0, B0I1S0, Q8WVS4, Q96EX3, Q8TCX1, Q9NP97, P63167
- Ligands
- ADP, ATP, MG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 8 distinct chains · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | O6-alkylguanine-DNA alkyltransferase MUTANT,DYNC2H1 variant PROTEIN,O6-alkylguanine-DNA alkyltransferase MUTANT,CYTOPLASMIC dynein 2 heavy chain 1,DYNC2H1 variant PROTEIN,DYNC2H1 variant PROTEIN,DYNC2H1 variant protein | protein | 3914 | 57% helix, 8% strand | E5BBQ0, B0I1S0 |
| B | O6-alkylguanine-DNA alkyltransferase MUTANT,DYNC2H1 variant PROTEIN,O6-alkylguanine-DNA alkyltransferase MUTANT,CYTOPLASMIC dynein 2 heavy chain 1,DYNC2H1 variant PROTEIN,DYNC2H1 variant PROTEIN,DYNC2H1 variant protein | protein | 3930 | 57% helix, 8% strand | E5BBQ0, B0I1S0 |
| C | Wd repeat-containing protein 60 | protein | 494 | 9% helix, 33% strand | Q8WVS4 |
| D | Wd repeat-containing protein 34 | protein | 446 | 10% helix, 33% strand | Q96EX3 |
| E | Cytoplasmic dynein 2 light intermediate chain 1 | protein | 312 | 42% helix, 13% strand | Q8TCX1 |
| F | Cytoplasmic dynein 2 light intermediate chain 1 | protein | 310 | 43% helix, 13% strand | Q8TCX1 |
| G, H | Dynein light chain roadblock-type 1 | protein | 93 | 37% helix, 30% strand | Q9NP97 |
| I, J, K, L, M, N | Dynein light chain 1, cytoplasmic | protein | 86 | 38% helix, 44% strand | P63167 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, B
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
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 | 1073 | 0.81 | 0.83 | 163 | empty |
| 2 | 985 | 0.81 | 0.83 | 117 | empty |
| 3 | 789 | 0.81 | 0.84 | 112 | empty |
| 4 | 972 | 0.80 | 0.82 | 141 | empty |
| 5 | 753 | 0.80 | 0.84 | 98 | empty |
Interfaces
29 interfaces between chains.
- A–B · 1441 Ų buried · 2 hydrogen bonds · protein-protein
- I–J · 613 Ų buried · 17 hydrogen bonds · protein-protein
- K–L · 579 Ų buried · 16 hydrogen bonds · protein-protein
- M–N · 574 Ų buried · 16 hydrogen bonds · protein-protein
- B–F · 525 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6SC2 · Structure of the dynein-2 complex; IFT-train bound model · the same entry in another collection · chain N against N, 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 E5BBQ0
- Every structure of UniProt B0I1S0
- Every structure of UniProt Q8WVS4
- Every structure of UniProt Q96EX3
- Every structure of UniProt Q8TCX1
- Every structure of UniProt Q9NP97
- Every structure of UniProt P63167
- Elsewhere: RCSB PDB 6SC2 · PDBe 6SC2 · UniProt E5BBQ0 · UniProt B0I1S0 · UniProt Q8WVS4 · UniProt Q96EX3 · UniProt Q8TCX1 · UniProt Q9NP97 · UniProt P63167
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