MolNFT v1 · #176511 · protein
Crystal structure of T2R-ttl-cevipabulin-eribulin complex
7DP8 · Tubulin alpha-1B chain: “Crystal structure of T2R-ttl-cevipabulin-eribulin complex”. X-ray diffraction, 7 ligands (GTP, G2X, GDP), 20 pockets (best druggability 0.85). MolNFT v1 #176511 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7DP8
- Type
- protein
- Length
- 2,196 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, G2X, GDP, 6K9, ACP, CA, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 438 | 47% helix, 18% strand | Q2XVP4 |
| B | Tubulin beta chain | protein | 418 | 49% helix, 18% strand | A0A287AGU7 |
| C | Tubulin alpha-1B chain | protein | 440 | 45% helix, 17% strand | Q2XVP4 |
| D | Tubulin beta chain | protein | 426 | 45% helix, 19% strand | A0A287AGU7 |
| E | Stathmin-4 | protein | 123 | 68% helix, 13% strand | P63043 |
| F | Tubulin tyrosine ligase | protein | 351 | 30% helix, 21% strand | E1BQ43 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, C, D
- G2X · 6-[2,6-bis(fluoranyl)-4-[3-(methylamino) propoxy]phenyl]-5-chloranyl-N-[(2S)-1,1,1-tris(fluoranyl)propan-2-yl]-[1,2,4]triazolo[1,5-a]pyrimidin-7-amine · ligand · 2 copies · chains B, C
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- 6K9 · (1S,3S,6S,9S,12S,14R,16R,18S,20R,21R,22S,26R,29S,31R,32S,33R,35R,36S)-20-[(2S)-3-amino-2-hydroxypropyl]-21-methoxy-14-methyl-8,15-dimethylidene-2,19,30,34,37,39,40,41-octaoxanonacyclo[24.9.2.1~3,32~.1~3,33~.1~6,9~.1~12,16~.0~18,22~.0~29,36~.0~31,35~]hentetracontan-24-one (non-preferred name) · ligand · chains D
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
- CA · Calcium ion · metal · 6 copies · chains A, E, B, C
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, F
- GOL · Glycerol · additive · 2 copies · chains A, B, 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 844 | 0.85 | 0.87 | 85 | GDP, MG, G2X |
| 2 | 170 | 0.79 | 0.95 | 36 | GTP, MG |
| 3 | 1177 | 0.79 | 0.81 | 105 | MG, ACP |
| 4 | 159 | 0.79 | 0.95 | 30 | empty |
| 5 | 1186 | 0.78 | 0.80 | 102 | GTP, MG, G2X |
Interfaces
9 interfaces between chains.
- A–E · 1660 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1455 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1437 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1398 Ų buried · 20 hydrogen bonds · protein-protein
- A–F · 819 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7DP8 · Crystal structure of T2R-TTL-Cevipabulin-eribulin complex · 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 A0A287AGU7
- Every structure of UniProt P63043
- Every structure of UniProt E1BQ43
- Elsewhere: RCSB PDB 7DP8 · PDBe 7DP8 · UniProt Q2XVP4 · UniProt A0A287AGU7 · UniProt P63043 · UniProt E1BQ43
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