MolNFT v1 · #158820 · protein
Tubulin-RB3_SLD-ttl in complex with compound 10BB
6O5M · Tubulin alpha-1B chain: “Tubulin-RB3_SLD-ttl in complex with compound 10BB”. X-ray diffraction, 6 ligands (GTP, G8K, GDP), 20 pockets (best druggability 0.83). MolNFT v1 #158820 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6O5M
- Type
- protein
- Length
- 2,172 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
- Q2XVP4, A0A287AGU7, Q9H169, E1BQ43
- Ligands
- GTP, G8K, GDP, ACP, MG, CA
- Pockets
- 20 · best druggability 0.83
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 | 437 | 47% helix, 18% strand | Q2XVP4 |
| B | Tubulin beta-2B chain | protein | 427 | 48% helix, 19% strand | A0A287AGU7 |
| C | Tubulin alpha-1B chain | protein | 440 | 47% helix, 17% strand | Q2XVP4 |
| D | Tubulin beta-2B chain | protein | 421 | 48% helix, 20% strand | A0A287AGU7 |
| E | Stathmin-4 | protein | 120 | 76% helix, 14% strand | Q9H169 |
| F | Tubulin tyrosine ligase | protein | 327 | 31% helix, 22% strand | E1BQ43 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, C, D
- G8K · [2-(1H-indol-4-yl)-1H-imidazol-4-yl](3,4,5-trimethoxyphenyl)methanone · ligand · 2 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D, F
- CA · Calcium ion · metal · 2 copies · chains A, C
- GOL · Glycerol · additive · 2 copies · chains A, B, F
- 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 | 1109 | 0.83 | 0.84 | 127 | GTP, MG, G8K |
| 2 | 670 | 0.81 | 0.86 | 88 | GDP, MG |
| 3 | 162 | 0.80 | 0.96 | 31 | G8K |
| 4 | 703 | 0.80 | 0.84 | 90 | GOL |
| 5 | 188 | 0.78 | 0.93 | 36 | GTP, MG |
Interfaces
9 interfaces between chains.
- A–E · 1606 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1396 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1324 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 887 Ų buried · 15 hydrogen bonds · protein-protein
- A–F · 843 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
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 A0A287AGU7
- Every structure of UniProt Q9H169
- Every structure of UniProt E1BQ43
- Elsewhere: RCSB PDB 6O5M · PDBe 6O5M · UniProt Q2XVP4 · UniProt A0A287AGU7 · UniProt Q9H169 · UniProt E1BQ43
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