Research workbench
Tandem GerMN domains of the sporulation protein GerM from Bacillus subtilis
Analyse Tandem GerMN domains of the sporulation protein GerM from Bacillus subtilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GZB
- Type
- protein
- Length
- 1,135 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Bacillus subtilis subsp. subtilis str. 168
- Molecule
- Spore germination protein GerM
- UniProt
- P39072
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.1 · 4 distinct chains · 21% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spore germination protein GerM | protein | 287 | 21% helix, 31% strand | P39072 |
| B | Spore germination protein GerM | protein | 282 | 21% helix, 32% strand | P39072 |
| C | Spore germination protein GerM | protein | 284 | 21% helix, 30% strand | P39072 |
| D | Spore germination protein GerM | protein | 282 | 21% helix, 31% strand | P39072 |
Ligands and binding sites
- ACT · Acetate ion · additive · 10 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1090 | 0.80 | 0.81 | 88 | empty |
| 2 | 802 | 0.78 | 0.82 | 64 | empty |
| 3 | 994 | 0.77 | 0.79 | 104 | empty |
| 4 | 661 | 0.73 | 0.80 | 69 | empty |
| 5 | 556 | 0.65 | 0.76 | 68 | empty |
Interfaces
5 interfaces between chains.
- C–D · 900 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 883 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 812 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 412 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 46 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6GZB · Tandem germn domains of the sporulation protein germ from bacillus subtilis · the same entry in another collection · chain D against D, TM-score 1.00
- P39072 · AlphaFold monomer V2.0 prediction for spore germination protein germ (P39072) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P39072
- Elsewhere: RCSB PDB 6GZB · PDBe 6GZB · UniProt P39072
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