Research workbench
Crystal structure of smba in complex with C-di-gmp
Analyse Crystal structure of smba in complex with C-di-gmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GS8
- Type
- protein
- Length
- 1,738 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- Q9A5E6
- Ligands
- C2E, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uncharacterized protein | protein | 301 | 42% helix, 17% strand | Q9A5E6 |
| C, D, E, F | Uncharacterized protein | protein | 284 | 38% helix, 18% strand | Q9A5E6 |
Ligands and binding sites
- C2E · 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10, 12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3, 2-D:3',2'-J][1,3,7,9,2, 8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) · ligand · 12 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 996 | 0.82 | 0.83 | 101 | empty |
| 2 | 1027 | 0.81 | 0.82 | 107 | C2E |
| 3 | 833 | 0.80 | 0.83 | 93 | empty |
| 4 | 243 | 0.57 | 0.78 | 39 | empty |
| 5 | 254 | 0.56 | 0.77 | 38 | empty |
Interfaces
6 interfaces between chains.
- C–D · 988 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 967 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 936 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 413 Ų buried · 5 hydrogen bonds · protein-protein
- A–F · 373 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 6GS8 · Crystal structure of SmbA in complex with c-di-GMP · the same entry in another collection · 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 Q9A5E6
- Elsewhere: RCSB PDB 6GS8 · PDBe 6GS8 · UniProt Q9A5E6
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