Research workbench
Cryo-EM structure of C. elegans GDP-microtubule
Analyse Cryo-EM structure of C. elegans GDP-microtubule in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E88
- Type
- protein
- Length
- 5,160 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-2 chain; Tubulin beta-2 chain
- UniProt
- P34690, P52275
- Ligands
- GTP, GDP
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 2 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, H, L, I, M | Tubulin alpha-2 chain | protein | 434 | 41% helix, 14% strand | P34690 |
| B, D, J, N, K, O | Tubulin beta-2 chain | protein | 426 | 45% helix, 17% strand | P52275 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 6 copies · chains A, B, C, D, H, J, L, N, I, K, M, O
- GDP · Guanosine-5'-diphosphate · ligand · 6 copies · chains B, C, D, J, L, N, K, M, O
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 | 498 | 0.87 | 0.94 | 69 | GTP |
| 2 | 500 | 0.87 | 0.93 | 64 | GTP |
| 3 | 519 | 0.87 | 0.93 | 72 | GTP |
| 4 | 747 | 0.86 | 0.89 | 99 | GDP |
| 5 | 498 | 0.86 | 0.92 | 64 | GTP |
Interfaces
17 interfaces between chains.
- C–D · 2043 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2033 Ų buried · 24 hydrogen bonds · protein-protein
- I–K · 2027 Ų buried · 25 hydrogen bonds · protein-protein
- H–J · 2025 Ų buried · 21 hydrogen bonds · protein-protein
- M–O · 2021 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6E88 · Cryo-EM structure of C. elegans GDP-microtubule · the same entry in another collection · chain O against O, 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 P34690
- Every structure of UniProt P52275
- Elsewhere: RCSB PDB 6E88 · PDBe 6E88 · UniProt P34690 · UniProt P52275
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