Research workbench
Crystal structure of the gsuk rck domain
Analyse Crystal structure of the gsuk rck domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GVL
- Type
- protein
- Length
- 1,820 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trka domain protein
- UniProt
- Q74FS9
- Ligands
- AMP, ZN, CA
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Trka domain protein | protein | 455 | 36% helix, 23% strand | Q74FS9 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, D, C
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 | 782 | 0.74 | 0.79 | 76 | empty |
| 2 | 704 | 0.73 | 0.79 | 61 | empty |
| 3 | 828 | 0.72 | 0.77 | 68 | empty |
| 4 | 536 | 0.72 | 0.80 | 32 | empty |
| 5 | 835 | 0.71 | 0.76 | 63 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1084 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1055 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1043 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1032 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 10 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4GVL · Crystal Structure of the GsuK RCK domain · 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 Q74FS9
- Elsewhere: RCSB PDB 4GVL · PDBe 4GVL · UniProt Q74FS9
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