Research workbench
Crystal structure of GTPase domain of human septin 12 in complex with gmppnp
Analyse Crystal structure of GTPase domain of human septin 12 in complex with gmppnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MQ9
- Type
- protein
- Length
- 1,057 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Septin-12
- UniProt
- Q8IYM1
- Ligands
- GNP, MG
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Septin-12 | protein | 265 | 42% helix, 22% strand | Q8IYM1 |
| B | Septin-12 | protein | 267 | 40% helix, 21% strand | Q8IYM1 |
| C | Septin-12 | protein | 264 | 40% helix, 21% strand | Q8IYM1 |
| D | Septin-12 | protein | 261 | 39% helix, 22% strand | Q8IYM1 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · 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
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.77 | 0.96 | 26 | empty |
| 2 | 469 | 0.68 | 0.80 | 61 | GNP, MG |
| 3 | 110 | 0.68 | 0.91 | 28 | empty |
| 4 | 263 | 0.64 | 0.82 | 43 | GNP, MG |
| 5 | 342 | 0.60 | 0.77 | 49 | GNP, MG |
Interfaces
6 interfaces between chains.
- A–D · 1513 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 322 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 306 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 174 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 38 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 6MQ9 · PDBe 6MQ9 · UniProt Q8IYM1
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