Research workbench
Human septin hexameric complex SEPT2G/SEPT6/SEPT7 by single particle cryo-EM
Analyse Human septin hexameric complex SEPT2G/SEPT6/SEPT7 by single particle cryo-EM in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M6J
- Type
- protein
- Length
- 1,614 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Septin-2; Septin-6; Septin-7
- UniProt
- Q15019, Q14141, Q16181
- Ligands
- GDP, GTP, MG
- Pockets
- 17 · best druggability 0.84
Structure
electron microscopy · 6 distinct chains · 35% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Septin-2 | protein | 234 | 37% helix, 9% strand | Q15019 |
| B | Septin-6 | protein | 287 | 31% helix, 14% strand | Q14141 |
| C | Septin-7 | protein | 270 | 37% helix, 17% strand | Q16181 |
| D | Septin-7 | protein | 273 | 35% helix, 18% strand | Q16181 |
| E | Septin-6 | protein | 296 | 33% helix, 16% strand | Q14141 |
| F | Septin-2 | protein | 254 | 37% helix, 16% strand | Q15019 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D, E, F
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B, E, F
- MG · Magnesium ion · metal · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 308 | 0.84 | 0.95 | 45 | empty |
| 2 | 800 | 0.82 | 0.85 | 83 | GDP |
| 3 | 315 | 0.82 | 0.93 | 45 | empty |
| 4 | 1107 | 0.77 | 0.79 | 77 | empty |
| 5 | 1116 | 0.75 | 0.78 | 71 | empty |
Interfaces
5 interfaces between chains.
- D–E · 2672 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 2281 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 1890 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1747 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1308 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7M6J · Human Septin Hexameric Complex SEPT2G/SEPT6/SEPT7 by Single Particle Cryo-EM · the same entry in another collection · chain F against F, TM-score 1.00
- Q15019 · AlphaFold monomer V2.0 prediction for septin-2 (Q15019) · a predicted model of the same protein · chain F against A, TM-score 0.97
- Q14141 · AlphaFold monomer V2.0 prediction for septin-6 (Q14141) · a predicted model of the same protein · chain B against A, TM-score 0.96
- Q16181 · AlphaFold monomer V2.0 prediction for septin-7 (Q16181) · a predicted model of the same protein · chain D against A, TM-score 0.92
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 Q14141
- Every structure of UniProt Q16181
- Elsewhere: RCSB PDB 7M6J · PDBe 7M6J · UniProt Q15019 · UniProt Q14141 · UniProt Q16181
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