Research workbench
Crystal structure of GTPase domain of human septin 2 / septin 8 heterocomplex
Analyse Crystal structure of GTPase domain of human septin 2 / septin 8 heterocomplex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UPR
- Type
- protein
- Length
- 537 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Septin-2; Septin-8
- UniProt
- Q15019, Q92599
- Ligands
- GDP, GTP, MG
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Septin-2 | protein | 267 | 39% helix, 19% strand | Q15019 |
| B | Septin-8 | protein | 270 | 39% helix, 21% strand | Q92599 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A, B
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- MG · Magnesium ion · metal · chains 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 | 132 | 0.78 | 0.96 | 40 | empty |
| 2 | 402 | 0.68 | 0.81 | 48 | GTP, MG |
| 3 | 149 | 0.64 | 0.86 | 28 | empty |
| 4 | 285 | 0.60 | 0.79 | 44 | GDP |
| 5 | 62 | 0.31 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1913 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6UPR · Crystal Structure of GTPase Domain of Human Septin 2 / Septin 8 Heterocomplex · the same entry in another collection · chain A against A, TM-score 1.00
- Q15019 · AlphaFold monomer V2.0 prediction for septin-2 (Q15019) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q92599 · AlphaFold monomer V2.0 prediction for septin-8 (Q92599) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q15019
- Every structure of UniProt Q92599
- Elsewhere: RCSB PDB 6UPR · PDBe 6UPR · UniProt Q15019 · UniProt Q92599
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