Research workbench
Structures of a beta-lactam bridged analogue in complex with tubulin
Analyse Structures of a beta-lactam bridged analogue in complex with tubulin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GON
- Type
- protein
- Length
- 2,162 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; Uncharacterized protein
- UniProt
- P81947, Q6B856, P63043, E1BQ43
- Ligands
- GTP, GDP, 6ZR, MG, CA
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 6 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 439 | 46% helix, 18% strand | P81947 |
| B | Tubulin beta-2B chain | protein | 422 | 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 | 71% helix, 14% strand | P63043 |
| F | Uncharacterized protein | protein | 319 | 28% helix, 20% strand | E1BQ43 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, D
- 6ZR · (3R,4R)-4-(4-methoxy-3-oxidanyl-phenyl)-3-methyl-1-(3,4,5-trimethoxyphenyl)azetidin-2-one · ligand · chains A, B
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, F
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 12 copies · chains A, F, E, B, C, D
- IMD · Imidazole · additive · 3 copies · chains C, D, E
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1083 | 0.88 | 0.89 | 130 | GTP, MG, 6ZR |
| 2 | 345 | 0.85 | 0.94 | 66 | GTP, MG |
| 3 | 611 | 0.81 | 0.86 | 78 | GDP, MG, GOL |
| 4 | 945 | 0.74 | 0.77 | 68 | GOL |
| 5 | 340 | 0.73 | 0.85 | 48 | GOL |
Interfaces
9 interfaces between chains.
- A–E · 1608 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1456 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1339 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 890 Ų buried · 14 hydrogen bonds · protein-protein
- C–E · 825 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5GON · Structures of a beta-lactam bridged analogue in complex with tubulin · 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 5GON · PDBe 5GON · UniProt P81947 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43
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