Research workbench
Crystal structure of the complex of ntca with its transcriptional co-activator pipx
Analyse Crystal structure of the complex of ntca with its transcriptional co-activator… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XKO
- Type
- protein
- Length
- 594 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Global nitrogen regulator; Pipx
- UniProt
- P29283, Q7X386
- Ligands
- AKG
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Global nitrogen regulator | protein | 212 | 42% helix, 28% strand | P29283 |
| C | Pipx | protein | 85 | 39% helix, 32% strand | Q7X386 |
| D | Pipx | protein | 85 | 39% helix, 32% strand | Q7X386 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.77 | 0.98 | 22 | empty |
| 2 | 80 | 0.74 | 0.97 | 19 | empty |
| 3 | 58 | 0.71 | 0.97 | 22 | empty |
| 4 | 193 | 0.68 | 0.86 | 26 | empty |
| 5 | 212 | 0.66 | 0.84 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2195 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 813 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 810 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 443 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 440 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2XKO · Crystal structure of the complex of NtcA with its transcriptional co- activator PipX · the same entry in another collection · chain A against A, TM-score 1.00
- P29283 · AlphaFold monomer V2.0 prediction for global nitrogen regulator (P29283) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P29283
- Every structure of UniProt Q7X386
- Elsewhere: RCSB PDB 2XKO · PDBe 2XKO · UniProt P29283 · UniProt Q7X386
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