MolNFT v1 · #125968 · protein
Dz-2384 tubulin complex
5LOV · Tubulin alpha-1B chain: “Dz-2384 tubulin complex”. X-ray diffraction, 6 ligands (GTP, GDP, 71E), 20 pockets (best druggability 0.83). MolNFT v1 #125968 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5LOV
- Type
- protein
- Length
- 2,128 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, 71E, ACP, MG, CA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 437 | 45% helix, 18% strand | P81947 |
| B | Tubulin beta-2B chain | protein | 417 | 48% helix, 19% strand | Q6B856 |
| C | Tubulin alpha-1B chain | protein | 437 | 48% helix, 17% strand | P81947 |
| D | Tubulin beta-2B chain | protein | 422 | 48% helix, 18% strand | Q6B856 |
| E | Stathmin-4 | protein | 117 | 78% helix, 13% strand | P63043 |
| F | Tubulin-tyrosine ligase | protein | 298 | 29% 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
- 71E · Dz 2384 · ligand · chains B, C
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
- MG · Magnesium ion · metal · 3 copies · chains A, B, C, D
- CA · Calcium ion · metal · chains A
- 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 904 | 0.83 | 0.85 | 95 | GDP, MG, 71E |
| 2 | 1031 | 0.80 | 0.81 | 108 | GTP, MG |
| 3 | 547 | 0.77 | 0.84 | 71 | GTP, MG |
| 4 | 749 | 0.77 | 0.81 | 68 | empty |
| 5 | 162 | 0.74 | 0.92 | 27 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1496 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1431 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1371 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1299 Ų buried · 20 hydrogen bonds · protein-protein
- C–E · 833 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5LOV · DZ-2384 tubulin complex · the same entry in another collection · chain E against E, TM-score 1.00
- Q6B856 · AlphaFold monomer V2.0 prediction for tubulin beta-2B chain (Q6B856) · a predicted model of the same protein · chain D against A, TM-score 0.99
- P81947 · AlphaFold monomer V2.0 prediction for tubulin alpha-1B chain (P81947) · a predicted model of the same protein · chain C against A, TM-score 0.96
- P63043 · AlphaFold monomer V2.0 prediction for stathmin-4 (P63043) · a predicted model of the same protein · chain E against A, TM-score 0.73
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 5LOV · PDBe 5LOV · UniProt P81947 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43
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