Research workbench
Complex of human tuba C-terminal SH3 domain and mena proline-rich peptide - H3
Analyse Complex of human tuba C-terminal SH3 domain and mena proline-rich peptide - H3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CC3
- Type
- protein
- Length
- 294 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dynamin-binding protein; Protein enabled homolog
- UniProt
- Q6XZF7, Q03173
- Ligands
- CL
- Pockets
- 6 · best druggability 0.47
Structure
x-ray diffraction · 5 distinct chains · 5% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dynamin-binding protein | protein | 61 | 5% helix, 44% strand | Q6XZF7 |
| B, D, F, H | Protein enabled homolog | protein | 12 | 0% helix, 0% strand | Q03173 |
| C | Dynamin-binding protein | protein | 64 | 5% helix, 42% strand | Q6XZF7 |
| E | Dynamin-binding protein | protein | 60 | 5% helix, 45% strand | Q6XZF7 |
| G | Dynamin-binding protein | protein | 61 | 5% helix, 44% strand | Q6XZF7 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains A, C, E
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.47 | 0.81 | 22 | empty |
| 2 | 97 | 0.46 | 0.80 | 18 | empty |
| 3 | 98 | 0.42 | 0.78 | 20 | empty |
| 4 | 61 | 0.41 | 0.81 | 16 | CL |
| 5 | 53 | 0.40 | 0.82 | 18 | empty |
Interfaces
10 interfaces between chains.
- E–F · 591 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 581 Ų buried · 5 hydrogen bonds · protein-protein
- G–H · 581 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 574 Ų buried · 5 hydrogen bonds · protein-protein
- E–G · 333 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4CC3 · Complex of human Tuba C-terminal SH3 domain and Mena proline-rich peptide - H3 · the same entry in another collection · chain H against H, TM-score 1.00
- Q6XZF7 · AlphaFold monomer V2.0 prediction for dynamin-binding protein (Q6XZF7) · a predicted model of the same protein · chain G against A, TM-score 0.95
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 Q6XZF7
- Every structure of UniProt Q03173
- Elsewhere: RCSB PDB 4CC3 · PDBe 4CC3 · UniProt Q6XZF7 · UniProt Q03173
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