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Crystal structure of a putative pii-like signaling protein (YP_323533.1) from anabaena variabilis atcc 29413 at 2.35 a resolution
Analyse Crystal structure of a putative pii-like signaling protein (YP_323533.1) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DFE
- Type
- protein
- Length
- 490 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative pii-like signaling protein
- UniProt
- Q3M8P8
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 36% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative pii-like signaling protein | protein | 82 | 35% helix, 45% strand | Q3M8P8 |
| B, D | Putative pii-like signaling protein | protein | 83 | 35% helix, 46% strand | Q3M8P8 |
| C | Putative pii-like signaling protein | protein | 81 | 36% helix, 44% strand | Q3M8P8 |
| E | Putative pii-like signaling protein | protein | 81 | 37% helix, 42% strand | Q3M8P8 |
| F | Putative pii-like signaling protein | protein | 80 | 35% helix, 41% strand | Q3M8P8 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 960 | 0.75 | 0.79 | 74 | empty |
| 2 | 174 | 0.52 | 0.78 | 32 | empty |
| 3 | 118 | 0.47 | 0.79 | 23 | empty |
| 4 | 120 | 0.46 | 0.78 | 20 | empty |
| 5 | 131 | 0.45 | 0.77 | 24 | empty |
Interfaces
9 interfaces between chains.
- A–B · 721 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 716 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 711 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 707 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 704 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3DFE · Crystal structure of a Putative Pii-Like Signaling Protein (YP_323533.1) from ANABAENA… · 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 Q3M8P8
- Elsewhere: RCSB PDB 3DFE · PDBe 3DFE · UniProt Q3M8P8
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