Research workbench
13PF E254A microtubule from recombinant human tubulin decorated with EB3
Analyse 13PF E254A microtubule from recombinant human tubulin decorated with EB3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SJ9
- Type
- protein
- Length
- 5,446 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta-3 chain; Microtubule-associated protein RP/EB family…
- UniProt
- P68363, Q13509, Q9UPY8
- Ligands
- GTP, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, J, K, L | Tubulin alpha-1B chain | protein | 435 | 44% helix, 17% strand | P68363 |
| B, D, F, G, H, I | Tubulin beta-3 chain | protein | 429 | 48% helix, 18% strand | Q13509 |
| M, N | Microtubule-associated protein RP/EB family member 3 | protein | 131 | 56% helix, 0% strand | Q9UPY8 |
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, B, C, D, E, F, G, H, I, 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 | 355 | 0.86 | 0.95 | 57 | GTP, MG |
| 2 | 367 | 0.86 | 0.95 | 54 | GTP, MG |
| 3 | 352 | 0.85 | 0.94 | 54 | GTP, MG |
| 4 | 1054 | 0.84 | 0.85 | 98 | empty |
| 5 | 1182 | 0.84 | 0.85 | 113 | empty |
Interfaces
25 interfaces between chains.
- B–K · 2012 Ų buried · 35 hydrogen bonds · protein-protein
- C–I · 2012 Ų buried · 33 hydrogen bonds · protein-protein
- D–L · 2004 Ų buried · 35 hydrogen bonds · protein-protein
- E–G · 2003 Ų buried · 35 hydrogen bonds · protein-protein
- A–H · 1997 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 7SJ9 · 13pf E254A microtubule from recombinant human tubulin decorated with EB3 · the same entry in another collection · chain N against N, 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
- Every structure of UniProt Q9UPY8
- Elsewhere: RCSB PDB 7SJ9 · PDBe 7SJ9 · UniProt P68363 · UniProt Q13509 · UniProt Q9UPY8
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