Research workbench
CPAP:TUBULIN:IE5 alpharep complex
Analyse CPAP:TUBULIN:IE5 alpharep complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Q1F
- Type
- protein
- Length
- 2,561 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha chain; Tubulin beta chain; IE5 alpharep; Centromere protein J
- UniProt
- A0A6P7DY20, A0A6P3TCJ9
- Ligands
- GTP, GDP, MG, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 9 distinct chains · 57% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, R | Tubulin alpha chain | protein | 432 | 45% helix, 18% strand | A0A6P7DY20 |
| B | Tubulin beta chain | protein | 430 | 48% helix, 20% strand | A0A6P3TCJ9 |
| C | IE5 alpharep | protein | 217 | 79% helix, 0% strand | — |
| D | IE5 alpharep | protein | 160 | 71% helix, 0% strand | — |
| P | Centromere protein J | protein | 50 | 38% helix, 6% strand | — |
| S | Tubulin beta chain | protein | 431 | 48% helix, 20% strand | A0A6P3TCJ9 |
| T | IE5 alpharep | protein | 220 | 78% helix, 0% strand | — |
| U | IE5 alpharep | protein | 147 | 75% helix, 0% strand | — |
| V | Centromere protein J | protein | 42 | 38% helix, 5% strand | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B, R, S
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, P, S, V
- MG · Magnesium ion · metal · 2 copies · chains A, B, R, S
- SO4 · Sulfate ion · ion · 2 copies · chains A, R
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A, B, P, R, S, V
- FLC · Citrate anion · additive · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1067 | 0.83 | 0.84 | 98 | GTP, MG |
| 2 | 477 | 0.77 | 0.85 | 60 | GTP, MG |
| 3 | 299 | 0.68 | 0.83 | 41 | empty |
| 4 | 527 | 0.68 | 0.78 | 59 | empty |
| 5 | 541 | 0.68 | 0.78 | 49 | empty |
Interfaces
14 interfaces between chains.
- B–P · 1718 Ų buried · 28 hydrogen bonds · protein-protein
- S–V · 1617 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1393 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1382 Ų buried · 17 hydrogen bonds · protein-protein
- R–S · 1380 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 7Q1F · CPAP:TUBULIN:IE5 alpharep 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 A0A6P7DY20
- Every structure of UniProt A0A6P3TCJ9
- Elsewhere: RCSB PDB 7Q1F · PDBe 7Q1F · UniProt A0A6P7DY20 · UniProt A0A6P3TCJ9
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