Research workbench
Crystal structure of GTPase domain of human septin 12 in complex with GDP
Analyse Crystal structure of GTPase domain of human septin 12 in complex with GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MQK
- Type
- protein
- Length
- 1,055 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Septin-12
- UniProt
- Q8IYM1
- Ligands
- GDP, MG
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Septin-12 | protein | 261 | 39% helix, 20% strand | Q8IYM1 |
| B | Septin-12 | protein | 265 | 40% helix, 19% strand | Q8IYM1 |
| C | Septin-12 | protein | 262 | 41% helix, 19% strand | Q8IYM1 |
| D | Septin-12 | protein | 267 | 40% helix, 19% strand | Q8IYM1 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, D, B, C
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.78 | 0.96 | 28 | empty |
| 2 | 879 | 0.76 | 0.80 | 115 | GDP, MG |
| 3 | 434 | 0.68 | 0.80 | 55 | GDP, MG |
| 4 | 404 | 0.62 | 0.77 | 45 | empty |
| 5 | 96 | 0.49 | 0.82 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1478 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 432 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 271 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 213 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 61 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 Q8IYM1
- Elsewhere: RCSB PDB 6MQK · PDBe 6MQK · UniProt Q8IYM1
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