Research workbench
Crystal structure of cpap PN2-3 C-terminal loop-helix in complex with darpin-tubulin
Analyse Crystal structure of cpap PN2-3 C-terminal loop-helix in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EIB
- Type
- protein
- Length
- 1,030 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta-2B chain; Designed ankyrin repeat protein; Peptide…
- UniProt
- P81947, Q6B856, Q9HC77
- Ligands
- GTP, MG
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Tubulin alpha-1B chain | protein | 429 | 46% helix, 18% strand | P81947 |
| D | Tubulin beta-2B chain | protein | 430 | 48% helix, 20% strand | Q6B856 |
| E | Designed ankyrin repeat protein | protein | 156 | 54% helix, 0% strand | — |
| F | Peptide from centromere protein J | protein | 15 | 40% helix, 7% strand | Q9HC77 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains C, D
- MG · Magnesium ion · metal · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 485 | 0.80 | 0.87 | 61 | GTP, MG |
| 2 | 461 | 0.68 | 0.80 | 44 | empty |
| 3 | 461 | 0.68 | 0.79 | 72 | empty |
| 4 | 201 | 0.60 | 0.82 | 37 | GTP, MG |
| 5 | 222 | 0.59 | 0.80 | 31 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1391 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 918 Ų buried · 6 hydrogen bonds · protein-protein
- D–F · 768 Ų buried · 14 hydrogen bonds · protein-protein
- C–F · 140 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5EIB · Crystal structure of CPAP PN2-3 C-terminal loop-helix in complex with DARPin-tubulin · the same entry in another collection · chain C against C, TM-score 1.00
- Q9HC77 · AlphaFold monomer V2.0 prediction for centromere protein J (Q9HC77) · a predicted model of the same protein · chain F against A, TM-score 0.32
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 Q6B856
- Every structure of UniProt Q9HC77
- Elsewhere: RCSB PDB 5EIB · PDBe 5EIB · UniProt P81947 · UniProt Q6B856 · UniProt Q9HC77
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