MolNFT v1 · #139639 · protein
The crystal structure of tubulin in complex with 4'- demethylepipodophyllotoxin
5XLT · Tubulin alpha-1B chain: “The crystal structure of tubulin in complex with 4'- demethylepipodophyllotoxin”. X-ray diffraction, 6 ligands (GTP, GDP, 89O), 20 pockets (best druggability 0.85). MolNFT v1 #139639 on GenesisL1: 3D…
- PDB
- 5XLT
- 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, GDP, 89O, 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 | 45% helix, 18% strand | P81947 |
| D | Tubulin beta-2B chain | protein | 421 | 49% helix, 18% 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 · 2 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, D
- 89O · (5S,5aR,8aR,9R)-9-(3,5-dimethoxy-4-oxidanyl-phenyl)-5-oxidanyl-5a,6,8a,9-tetrahydro-5H-[2]benzofuro[6,5-f][1,3]benzodioxol-8-one · ligand · 2 copies · chains A, B, C, D
- 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 958 | 0.85 | 0.86 | 124 | GDP, MG |
| 2 | 840 | 0.83 | 0.85 | 92 | GTP, MG, 89O |
| 3 | 470 | 0.80 | 0.88 | 59 | 89O |
| 4 | 602 | 0.78 | 0.84 | 76 | GTP, MG |
| 5 | 174 | 0.75 | 0.92 | 37 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1570 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1420 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1342 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 903 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 844 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5XLT · The crystal structure of tubulin in complex with 4'-demethylepipodophyllotoxin · 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 5XLT · PDBe 5XLT · UniProt P81947 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43
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