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Crystal structure of SIGM54 activator (aaa+ ATPase) in the active state
Analyse Crystal structure of SIGM54 activator (aaa+ ATPase) in the active state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NY6
- Type
- protein
- Length
- 3,456 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator (ntrc family)
- UniProt
- O67198
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 45% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, I, J, M, N | Transcriptional regulator (ntrc family) | protein | 247 | 47% helix, 15% strand | O67198 |
| B | Transcriptional regulator (ntrc family) | protein | 243 | 47% helix, 9% strand | O67198 |
| C, E, F, G, K | Transcriptional regulator (ntrc family) | protein | 248 | 46% helix, 13% strand | O67198 |
| H | Transcriptional regulator (ntrc family) | protein | 245 | 43% helix, 11% strand | O67198 |
| L | Transcriptional regulator (ntrc family) | protein | 246 | 44% helix, 14% strand | O67198 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 14 copies · chains B, C, D, E, F, G, A, H, I, J, K, L, M, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.80 | 0.81 | 103 | ADP |
| 2 | 803 | 0.79 | 0.82 | 88 | ADP |
| 3 | 894 | 0.78 | 0.81 | 89 | ADP |
| 4 | 756 | 0.77 | 0.82 | 61 | ADP |
| 5 | 652 | 0.77 | 0.83 | 77 | ADP |
Interfaces
23 interfaces between chains.
- F–G · 1498 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1425 Ų buried · 14 hydrogen bonds · protein-protein
- L–M · 1414 Ų buried · 17 hydrogen bonds · protein-protein
- H–I · 1399 Ų buried · 18 hydrogen bonds · protein-protein
- H–N · 1394 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1NY6 · Crystal structure of sigm54 activator (AAA+ ATPase) in the active state · 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 O67198
- Elsewhere: RCSB PDB 1NY6 · PDBe 1NY6 · UniProt O67198
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