Research workbench
Cryo-EM structure of the N-terminal dc repeat (ndc) of ndc-ndc chimera (human sequence) bound to 14-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
- 6RFD
- Type
- protein
- Length
- 1,821 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
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, a | Tubulin alpha-1B chain | protein | 432 | 43% helix, 15% strand | P81947 |
| B, b | Tubulin beta-2B chain | protein | 429 | 43% helix, 17% strand | Q6B856 |
| N | Neuronal migration protein doublecortin | protein | 99 | 12% helix, 20% strand | O43602 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, a
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B, a, b
- 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 354 | 0.85 | 0.94 | 50 | GDP |
| 2 | 481 | 0.83 | 0.90 | 71 | GDP |
| 3 | 835 | 0.80 | 0.83 | 82 | empty |
| 4 | 669 | 0.80 | 0.84 | 74 | empty |
| 5 | 461 | 0.78 | 0.86 | 59 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1884 Ų buried · 20 hydrogen bonds · protein-protein
- a–b · 1879 Ų buried · 19 hydrogen bonds · protein-protein
- A–a · 472 Ų buried · 5 hydrogen bonds · protein-protein
- b–N · 469 Ų buried · 2 hydrogen bonds · protein-protein
- B–N · 460 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6RFD · Cryo-EM structure of the N-terminal DC repeat (NDC) of NDC-NDC chimera (human sequence)… · 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 N against A, TM-score 0.89
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 6RFD · PDBe 6RFD · UniProt P81947 · UniProt Q6B856 · UniProt O43602
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