Research workbench
Undecorated 13PF E254N microtubule from recombinant human tubulin
Analyse Undecorated 13PF E254N microtubule from recombinant human tubulin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SJA
- Type
- protein
- Length
- 5,166 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta-3 chain
- UniProt
- P68363, Q13509
- Ligands
- GTP, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 2 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, J, K, L | Tubulin alpha-1B chain | protein | 432 | 46% helix, 18% strand | P68363 |
| B, D, F, G, H, I | Tubulin beta-3 chain | protein | 429 | 48% helix, 17% strand | Q13509 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 12 copies · chains A, H, B, C, I, D, E, G, F, J, K, L
- MG · Magnesium ion · metal · 12 copies · chains A, H, B, C, I, D, E, G, F, J, K, L
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 | 455 | 0.84 | 0.91 | 62 | GTP, MG |
| 2 | 260 | 0.83 | 0.95 | 45 | GTP, MG |
| 3 | 267 | 0.83 | 0.95 | 44 | GTP, MG |
| 4 | 1039 | 0.83 | 0.84 | 119 | GTP, MG |
| 5 | 257 | 0.82 | 0.94 | 44 | GTP, MG |
Interfaces
17 interfaces between chains.
- F–J · 1960 Ų buried · 18 hydrogen bonds · protein-protein
- A–H · 1955 Ų buried · 17 hydrogen bonds · protein-protein
- E–G · 1952 Ų buried · 19 hydrogen bonds · protein-protein
- D–L · 1946 Ų buried · 18 hydrogen bonds · protein-protein
- B–K · 1945 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 covalent (covalent ligand).
Compared structures
- 7SJA · Undecorated 13pf E254N microtubule from recombinant human tubulin · the same entry in another collection · chain L against L, 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 P68363
- Every structure of UniProt Q13509
- Elsewhere: RCSB PDB 7SJA · PDBe 7SJA · UniProt P68363 · UniProt Q13509
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