Research workbench
Cryo-EM structure of the C-terminal dc repeat (cdc) of human doublecortin (dcx) bound to 13-protofilament GDP.PI-microtubule
Analyse Cryo-EM structure of the C-terminal dc repeat (cdc) of human doublecortin (dcx)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RF2
- Type
- protein
- Length
- 1,809 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta-2B chain; Neuronal migration protein doublecortin
- UniProt
- P81947, Q6B856, O43602
- Ligands
- GTP, GDP, MG, PO4
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a, A | Tubulin alpha-1B chain | protein | 432 | 40% helix, 16% strand | P81947 |
| B, b | Tubulin beta-2B chain | protein | 429 | 41% helix, 17% strand | Q6B856 |
| C | Neuronal migration protein doublecortin | protein | 87 | 15% helix, 16% strand | O43602 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains a, A
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, A, a, b
- MG · Magnesium ion · metal · 2 copies · chains a, A
- PO4 · Phosphate ion · ion · 2 copies · chains a, b, B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 359 | 0.84 | 0.93 | 56 | GDP, PO4 |
| 2 | 357 | 0.84 | 0.93 | 53 | PO4, GDP |
| 3 | 1000 | 0.80 | 0.81 | 112 | empty |
| 4 | 887 | 0.79 | 0.82 | 83 | empty |
| 5 | 547 | 0.72 | 0.81 | 49 | empty |
Interfaces
8 interfaces between chains.
- a–b · 1965 Ų buried · 24 hydrogen bonds · protein-protein
- B–A · 1962 Ų buried · 25 hydrogen bonds · protein-protein
- a–A · 560 Ų buried · 3 hydrogen bonds · protein-protein
- B–b · 479 Ų buried · 4 hydrogen bonds · protein-protein
- a–C · 354 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6RF2 · Cryo-EM structure of the C-terminal DC repeat (CDC) of human doublecortin (DCX) bound to… · the same entry in another collection · chain a against a, TM-score 1.00
- O43602 · AlphaFold monomer V2.0 prediction for neuronal migration protein doublecortin (O43602) · a predicted model of the same protein · chain C against A, TM-score 0.87
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 P81947
- Every structure of UniProt Q6B856
- Every structure of UniProt O43602
- Elsewhere: RCSB PDB 6RF2 · PDBe 6RF2 · UniProt P81947 · UniProt Q6B856 · UniProt O43602
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