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Structure of a delta-N mutant - E232START - of PA1120 (tpbb or yfin) from pseudomonas aeruginosa (PAO1) comprising only the ggdef domain
Analyse Structure of a delta-N mutant - E232START - of PA1120 (tpbb or yfin) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A7E
- Type
- protein
- Length
- 520 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diguanylate cyclase tpbb
- UniProt
- Q9I4L5
- Ligands
- MG
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Diguanylate cyclase tpbb | protein | 172 | 47% helix, 24% strand | Q9I4L5 |
| B | Diguanylate cyclase tpbb | protein | 176 | 45% helix, 22% strand | Q9I4L5 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 184 | 0.51 | 0.77 | 29 | empty |
| 2 | 212 | 0.45 | 0.73 | 28 | MG |
| 3 | 122 | 0.45 | 0.77 | 20 | empty |
| 4 | 171 | 0.39 | 0.72 | 26 | MG |
Interfaces
2 interfaces between chains.
- A–B · 721 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 668 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 7A7E · Structure of a delta-N mutant - E232start - of PA1120 (TpbB or YfiN) from Pseudomonas… · 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 Q9I4L5
- Elsewhere: RCSB PDB 7A7E · PDBe 7A7E · UniProt Q9I4L5
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