Research workbench
Crystal structure of TD1-GATORBULIN1 complex
Analyse Crystal structure of TD1-GATORBULIN1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ALR
- Type
- protein
- Length
- 1,008 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta-3 chain; Designed ankyrin repeat protein (darpin) D1
- UniProt
- P81947, Q2T9S0
- Ligands
- GLY, GTP, RQK, GDP, MG, SO4
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 425 | 45% helix, 18% strand | P81947 |
| B | Tubulin beta-3 chain | protein | 428 | 49% helix, 19% strand | Q2T9S0 |
| F | Designed ankyrin repeat protein (darpin) D1 | protein | 155 | 55% helix, 0% strand | — |
Ligands and binding sites
- GLY · Glycine · ligand · chains A
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- RQK · (2~{R})-2-oxidanyl-2-[(6~{S},9~{S},12~{S},15~{S}, 17~{S})-6,10,12,17-tetramethyl-3-methylidene-7-oxidanyl-2,5,8,11,14-pentakis(oxidanylidene)-13-oxa-1, 4,7,10-tetrazabicyclo[13.3.0]octadecan-9-yl]ethanamide · ligand · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- MG · Magnesium ion · metal · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1152 | 0.80 | 0.82 | 112 | GTP, MG, RQK, SO4 |
| 2 | 159 | 0.61 | 0.84 | 28 | empty |
| 3 | 183 | 0.58 | 0.81 | 35 | GDP |
| 4 | 78 | 0.52 | 0.85 | 19 | empty |
| 5 | 52 | 0.51 | 0.88 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1416 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 953 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7ALR · Crystal structure of TD1-gatorbulin1 complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q2T9S0 · AlphaFold monomer V2.0 prediction for tubulin beta-3 chain (Q2T9S0) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P81947 · AlphaFold monomer V2.0 prediction for tubulin alpha-1B chain (P81947) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q2T9S0
- Elsewhere: RCSB PDB 7ALR · PDBe 7ALR · UniProt P81947 · UniProt Q2T9S0
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