Research workbench
High resolution human SEPTIN3 GTPase domain with alpha-zero helix in complex with GDP
Analyse High resolution human SEPTIN3 GTPase domain with alpha-zero helix in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Z54
- Type
- protein
- Length
- 542 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuronal-specific septin-3
- UniProt
- Q9UH03
- Ligands
- GDP, MG
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neuronal-specific septin-3 | protein | 273 | 38% helix, 20% strand | Q9UH03 |
| B | Neuronal-specific septin-3 | protein | 269 | 44% helix, 19% strand | Q9UH03 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.75 | 0.88 | 45 | GDP, MG |
| 2 | 113 | 0.73 | 0.94 | 30 | empty |
| 3 | 406 | 0.72 | 0.83 | 48 | GDP, MG |
| 4 | 94 | 0.64 | 0.90 | 25 | empty |
| 5 | 79 | 0.34 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1590 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 4Z54 · High Resolution Human Septin3 GTPase domain with alpha-zero helix in complex with GDP · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UH03 · AlphaFold monomer V2.0 prediction for neuronal-specific septin-3 (Q9UH03) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9UH03
- Elsewhere: RCSB PDB 4Z54 · PDBe 4Z54 · UniProt Q9UH03
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