Research workbench
Structure of mixed pii-ADP complexes from S. elongatus
Analyse Structure of mixed pii-ADP complexes from S. elongatus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4C3K
- Type
- protein
- Length
- 588 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrogen regulatory protein P-II
- UniProt
- P0A3F4
- Ligands
- ADP, PO4
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 32% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrogen regulatory protein P-II | protein | 98 | 35% helix, 38% strand | P0A3F4 |
| B | Nitrogen regulatory protein P-II | protein | 90 | 32% helix, 39% strand | P0A3F4 |
| C | Nitrogen regulatory protein P-II | protein | 98 | 27% helix, 38% strand | P0A3F4 |
| D | Nitrogen regulatory protein P-II | protein | 101 | 32% helix, 38% strand | P0A3F4 |
| E | Nitrogen regulatory protein P-II | protein | 96 | 33% helix, 40% strand | P0A3F4 |
| F | Nitrogen regulatory protein P-II | protein | 105 | 31% helix, 36% strand | P0A3F4 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, C, D, E, F
- PO4 · Phosphate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 167 | 0.81 | 0.97 | 28 | ADP |
| 2 | 182 | 0.78 | 0.94 | 37 | ADP |
| 3 | 897 | 0.74 | 0.78 | 64 | empty |
| 4 | 274 | 0.72 | 0.86 | 52 | ADP |
| 5 | 237 | 0.62 | 0.81 | 34 | ADP |
Interfaces
12 interfaces between chains.
- A–C · 1224 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1214 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1212 Ų buried · 27 hydrogen bonds · protein-protein
- D–F · 1173 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1102 Ų buried · 19 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 P0A3F4
- Elsewhere: RCSB PDB 4C3K · PDBe 4C3K · UniProt P0A3F4
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