Research workbench
Microtubule depolymerizing agent podophyllotoxin derivative YJTSF1
Analyse Microtubule depolymerizing agent podophyllotoxin derivative YJTSF1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JCB
- Type
- protein
- Length
- 2,153 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta chain; Stathmin; Tubulin-tyrosine ligase
- UniProt
- Q2XVP4, F2Z5B2, F2Z508
- Ligands
- GTP, GDP, NV4, ACP, MG, CA, NA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 439 | 46% helix, 18% strand | Q2XVP4 |
| B | Tubulin beta chain | protein | 423 | 50% helix, 19% strand | F2Z5B2 |
| C | Tubulin alpha-1B chain | protein | 440 | 48% helix, 17% strand | Q2XVP4 |
| D | Tubulin beta chain | protein | 418 | 50% helix, 19% strand | F2Z5B2 |
| E | Stathmin | protein | 121 | 76% helix, 14% strand | F2Z508 |
| F | Tubulin-tyrosine ligase | protein | 312 | 31% helix, 22% strand | — |
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
- NV4 · (5R,5aR,8aS,9R)-9-[(4H-1,2,4-triazol-3-yl)sulfanyl]-5-(3,4,5-trimethoxyphenyl)-5,8,8a,9-tetrahydro-2H-furo[3',4':6,7]naphtho[2,3-d][1,3]dioxol-6(5aH)-one · ligand · 2 copies · chains A, B, C, D
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D, F
- CA · Calcium ion · metal · 2 copies · chains A, C
- NA · Sodium ion · metal · 2 copies · chains B, C
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D
- IMD · Imidazole · additive · 2 copies · chains A, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 755 | 0.84 | 0.87 | 98 | GTP, MG, NV4 |
| 2 | 888 | 0.83 | 0.85 | 122 | GDP, MG, GOL |
| 3 | 991 | 0.83 | 0.84 | 96 | GTP, MG, NV4 |
| 4 | 388 | 0.81 | 0.89 | 63 | empty |
| 5 | 81 | 0.71 | 0.95 | 22 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1557 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1388 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1378 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 896 Ų buried · 15 hydrogen bonds · protein-protein
- C–E · 819 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 5JCB · Microtubule depolymerizing agent podophyllotoxin derivative YJTSF1 · 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 Q2XVP4
- Every structure of UniProt F2Z5B2
- Every structure of UniProt F2Z508
- Elsewhere: RCSB PDB 5JCB · PDBe 5JCB · UniProt Q2XVP4 · UniProt F2Z5B2 · UniProt F2Z508
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