Research workbench
The crystal structure of tubulin complexed with a benzylidene derivative of 9(10H)-anthracenone
Analyse The crystal structure of tubulin complexed with a benzylidene derivative of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XLZ
- Type
- protein
- Length
- 2,180 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta-2B chain; Stathmin-4; Tubulin tyrosine ligase
- UniProt
- P81947, Q6B856, P63043, E1BQ43
- Ligands
- GTP, 89U, GDP, ACP, MG, CA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 437 | 46% helix, 19% strand | P81947 |
| B | Tubulin beta-2B chain | protein | 427 | 45% helix, 19% strand | Q6B856 |
| C | Tubulin alpha-1B chain | protein | 440 | 46% helix, 17% strand | P81947 |
| D | Tubulin beta-2B chain | protein | 421 | 48% helix, 19% strand | Q6B856 |
| E | Stathmin-4 | protein | 121 | 76% helix, 13% strand | P63043 |
| F | Tubulin tyrosine ligase | protein | 334 | 31% helix, 21% strand | E1BQ43 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, C, D
- 89U · 10-[(4-methoxy-3-oxidanyl-phenyl)methylidene]anthracen-9-one · ligand · 2 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains A, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 584 | 0.85 | 0.91 | 80 | GTP, MG, 89U |
| 2 | 779 | 0.85 | 0.88 | 95 | GTP, MG, 89U |
| 3 | 662 | 0.81 | 0.86 | 89 | GDP, MG |
| 4 | 181 | 0.76 | 0.92 | 37 | empty |
| 5 | 315 | 0.72 | 0.85 | 42 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1581 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1426 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1388 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 906 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 836 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5XLZ · The crystal structure of tubulin complexed with a benzylidene derivative of… · the same entry in another collection · chain A against A, 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 P81947
- Every structure of UniProt Q6B856
- Every structure of UniProt P63043
- Every structure of UniProt E1BQ43
- Elsewhere: RCSB PDB 5XLZ · PDBe 5XLZ · UniProt P81947 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43
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