MolNFT v1 · #141357 · protein
Crystal structure of tubulin-stathmin-ttl-compound tca complex
5Z4P · Tubulin alpha-1B chain: “Crystal structure of tubulin-stathmin-ttl-compound tca complex”. X-ray diffraction, 6 ligands (GTP, GDP, 97O), 20 pockets (best druggability 0.88). MolNFT v1 #141357 on GenesisL1: 3D structure, binding sites…
- PDB
- 5Z4P
- Type
- protein
- Length
- 2,161 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, 97O, ACP, MG, CA
- Pockets
- 20 · best druggability 0.88
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 | 438 | 45% helix, 18% strand | P81947 |
| B | Tubulin beta-2B chain | protein | 424 | 49% helix, 18% strand | Q6B856 |
| C | Tubulin alpha-1B chain | protein | 440 | 47% 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 | 317 | 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
- 97O · 6,7,8-trimethoxy-1-(4-methoxyphenyl)-4,5-dihydro-2~{H}-benzo[e]indazole · ligand · chains A, B
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 11 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1086 | 0.88 | 0.89 | 142 | GTP, MG, 97O |
| 2 | 766 | 0.83 | 0.86 | 95 | GTP, MG, GOL |
| 3 | 1173 | 0.82 | 0.84 | 129 | GDP, GOL |
| 4 | 452 | 0.78 | 0.86 | 43 | ACP |
| 5 | 89 | 0.72 | 0.96 | 25 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1524 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1485 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1375 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 880 Ų buried · 13 hydrogen bonds · protein-protein
- C–E · 854 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5Z4P · Crystal structure of tubulin-stathmin-TTL-Compound TCA complex · the same entry in another collection · chain C against C, 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 5Z4P · PDBe 5Z4P · UniProt P81947 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43
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