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Crystal structure of the sixth or C-terminal SH3 domain of human tuba in complex with proline-rich peptides of N-wasp. space group P41
Analyse Crystal structure of the sixth or C-terminal SH3 domain of human tuba in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CC7
- Type
- protein
- Length
- 504 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dynamin-binding protein; Neural wiskott-aldrich syndrome protein
- UniProt
- Q6XZF7, O00401
- Ligands
- MG, CL
- Pockets
- 7 · best druggability 0.50
Structure
x-ray diffraction · 10 distinct chains · 5% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dynamin-binding protein | protein | 58 | 5% helix, 47% strand | Q6XZF7 |
| B | Neural wiskott-aldrich syndrome protein | protein | 10 | 0% helix, 0% strand | O00401 |
| C | Dynamin-binding protein | protein | 63 | 5% helix, 43% strand | Q6XZF7 |
| D, F, H, N | Neural wiskott-aldrich syndrome protein | protein | 12 | 0% helix, 0% strand | O00401 |
| E | Dynamin-binding protein | protein | 62 | 5% helix, 44% strand | Q6XZF7 |
| G | Dynamin-binding protein | protein | 61 | 5% helix, 44% strand | Q6XZF7 |
| I | Dynamin-binding protein | protein | 61 | 5% helix, 44% strand | Q6XZF7 |
| J, L | Neural wiskott-aldrich syndrome protein | protein | 11 | 0% helix, 0% strand | O00401 |
| K | Dynamin-binding protein | protein | 60 | 5% helix, 47% strand | Q6XZF7 |
| M | Dynamin-binding protein | protein | 59 | 5% helix, 47% strand | Q6XZF7 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains K, M
- CL · Chloride ion · ion · 17 copies · chains A, C, E, G, I, J, K, M
- GOL · Glycerol · additive · 4 copies · chains A, C, D, E, F, K, M, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 192 | 0.50 | 0.77 | 26 | empty |
| 2 | 116 | 0.49 | 0.81 | 24 | empty |
| 3 | 79 | 0.48 | 0.82 | 23 | GOL, CL |
| 4 | 81 | 0.46 | 0.81 | 17 | empty |
| 5 | 88 | 0.46 | 0.80 | 19 | empty |
Interfaces
21 interfaces between chains.
- G–H · 602 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 577 Ų buried · 6 hydrogen bonds · protein-protein
- I–J · 564 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 563 Ų buried · 9 hydrogen bonds · protein-protein
- M–N · 563 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4CC7 · Crystal structure of the sixth or C-terminal SH3 domain of human Tuba in complex with… · the same entry in another collection · chain M against M, 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 Q6XZF7
- Every structure of UniProt O00401
- Elsewhere: RCSB PDB 4CC7 · PDBe 4CC7 · UniProt Q6XZF7 · UniProt O00401
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