MolNFT v1 · #146122 · protein
Tubulin-RB3_SLD-ttl in complex with compound 13F
6D88 · Tubulin alpha-1B chain: “Tubulin-RB3_SLD-ttl in complex with compound 13F”. X-ray diffraction, 6 ligands (GTP, GDP, G9K), 20 pockets (best druggability 0.86). MolNFT v1 #146122 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6D88
- Type
- protein
- Length
- 2,178 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta chain; Stathmin-4; Tubulin tyrosine ligase
- UniProt
- Q2XVP4, A0A287AGU7, P63043, E1BQ43
- Ligands
- GTP, GDP, G9K, ACP, MG, CA
- Pockets
- 20 · best druggability 0.86
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 chain | protein | 427 | 48% helix, 20% strand | A0A287AGU7 |
| C | Tubulin alpha-1B chain | protein | 440 | 48% helix, 17% strand | Q2XVP4 |
| D | Tubulin beta chain | protein | 421 | 49% helix, 19% strand | A0A287AGU7 |
| E | Stathmin-4 | protein | 121 | 75% helix, 14% strand | P63043 |
| F | Tubulin tyrosine ligase | protein | 332 | 29% helix, 21% strand | E1BQ43 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, C, D
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, D
- G9K · [2-(1H-indol-3-yl)-1H-imidazol-4-yl](8-methoxy-1,4-benzodioxin-6-yl)methanone · ligand · 2 copies · chains A, B, C, D
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
- MG · Magnesium ion · metal · 3 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 365 | 0.86 | 0.95 | 63 | GTP, MG, G9K |
| 2 | 385 | 0.85 | 0.94 | 63 | GTP, MG, G9K |
| 3 | 1163 | 0.82 | 0.83 | 128 | GDP, MG |
| 4 | 152 | 0.78 | 0.95 | 36 | empty |
| 5 | 891 | 0.73 | 0.77 | 66 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1656 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1498 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1397 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 905 Ų buried · 13 hydrogen bonds · protein-protein
- C–E · 805 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6D88 · Tubulin-RB3_SLD-TTL in complex with compound 13f · the same entry in another collection · chain F against F, 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 A0A287AGU7
- Every structure of UniProt P63043
- Every structure of UniProt E1BQ43
- Elsewhere: RCSB PDB 6D88 · PDBe 6D88 · UniProt Q2XVP4 · UniProt A0A287AGU7 · UniProt P63043 · UniProt E1BQ43
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