Research workbench
Cryo-EM structure of the N-terminal dc repeat (ndc) of ndc-ndc chimera (human sequence) bound to 13-protofilament GDP-microtubule
Analyse Cryo-EM structure of the N-terminal dc repeat (ndc) of ndc-ndc chimera (human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RF8
- Type
- protein
- Length
- 1,821 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuronal migration protein doublecortin; Tubulin beta-2B chain; Tubulin alpha-1B chain
- UniProt
- O43602, Q6B856, P81947
- Ligands
- GDP, GTP, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| N | Neuronal migration protein doublecortin | protein | 99 | 13% helix, 18% strand | O43602 |
| b, B | Tubulin beta-2B chain | protein | 429 | 42% helix, 18% strand | Q6B856 |
| A, a | Tubulin alpha-1B chain | protein | 432 | 41% helix, 14% strand | P81947 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains b, a, A, B
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, a
- MG · Magnesium ion · metal · 2 copies · chains A, 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 361 | 0.85 | 0.94 | 56 | GDP |
| 2 | 349 | 0.84 | 0.93 | 51 | GDP |
| 3 | 1180 | 0.82 | 0.83 | 123 | empty |
| 4 | 783 | 0.79 | 0.83 | 79 | empty |
| 5 | 587 | 0.73 | 0.81 | 52 | empty |
Interfaces
8 interfaces between chains.
- b–a · 1893 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1829 Ų buried · 16 hydrogen bonds · protein-protein
- N–B · 505 Ų buried · 3 hydrogen bonds · protein-protein
- A–a · 466 Ų buried · 4 hydrogen bonds · protein-protein
- N–b · 457 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6RF8 · Cryo-EM structure of the N-terminal DC repeat (NDC) of NDC-NDC chimera (human sequence)… · the same entry in another collection · chain N against N, TM-score 1.00
- O43602 · AlphaFold monomer V2.0 prediction for neuronal migration protein doublecortin (O43602) · a predicted model of the same protein · chain N against A, TM-score 0.88
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 O43602
- Every structure of UniProt Q6B856
- Every structure of UniProt P81947
- Elsewhere: RCSB PDB 6RF8 · PDBe 6RF8 · UniProt O43602 · UniProt Q6B856 · UniProt P81947
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