Research workbench
Cytoplasmic dynein (A2) bound to BICDR1
Analyse Cytoplasmic dynein (A2) bound to BICDR1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Z8J
- Type
- protein
- Length
- 2,487 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bicd family-like cargo adapter 1; Cytoplasmic dynein 1 heavy chain 1; Cytoplasmic dynein…
- UniProt
- A0JNT9, Q14204, Q13409, O43237
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 7 distinct chains · 61% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X, x | Bicd family-like cargo adapter 1 | protein | 93 | 98% helix, 0% strand | A0JNT9 |
| f | Cytoplasmic dynein 1 heavy chain 1 | protein | 674 | 74% helix, 3% strand | Q14204 |
| h, o | Cytoplasmic dynein 1 intermediate chain 2 | protein | 358 | 4% helix, 44% strand | Q13409 |
| j | Cytoplasmic dynein 1 light intermediate chain 2 | protein | 247 | 52% helix, 9% strand | O43237 |
| m | Cytoplasmic dynein 1 heavy chain 1 | protein | 524 | 77% helix, 1% strand | Q14204 |
| n | Cytoplasmic dynein 1 heavy chain 1 | protein | 126 | 77% helix, 0% strand | Q14204 |
| r | Cytoplasmic dynein 1 light intermediate chain 2 | protein | 14 | 86% helix, 0% strand | O43237 |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 429 | 0.76 | 0.85 | 55 | empty |
| 2 | 79 | 0.74 | 0.97 | 19 | empty |
| 3 | 913 | 0.74 | 0.78 | 77 | empty |
| 4 | 652 | 0.74 | 0.80 | 57 | empty |
| 5 | 443 | 0.74 | 0.83 | 50 | empty |
Interfaces
16 interfaces between chains.
- X–x · 2344 Ų buried · 10 hydrogen bonds · protein-protein
- f–h · 2084 Ų buried · 22 hydrogen bonds · protein-protein
- m–o · 1801 Ų buried · 12 hydrogen bonds · protein-protein
- f–j · 1696 Ų buried · 10 hydrogen bonds · protein-protein
- f–m · 716 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7Z8J · Cytoplasmic dynein (A2) bound to BICDR1 · the same entry in another collection · chain x against x, TM-score 1.00
- Q13409 · AlphaFold monomer V2.0 prediction for cytoplasmic dynein 1 intermediate chain 2 (Q13409) · a predicted model of the same protein · chain h against A, TM-score 0.99
- A0JNT9 · AlphaFold monomer V2.0 prediction for bicd family-like cargo adapter 1 (A0JNT9) · a predicted model of the same protein · chain x against A, TM-score 0.90
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 A0JNT9
- Every structure of UniProt Q14204
- Every structure of UniProt Q13409
- Every structure of UniProt O43237
- Elsewhere: RCSB PDB 7Z8J · PDBe 7Z8J · UniProt A0JNT9 · UniProt Q14204 · UniProt Q13409 · UniProt O43237
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