Research workbench
Crystal structure of the gntr-type sialoregulator nanr from escherichia COLI, in complex with sialic acid
Analyse Crystal structure of the gntr-type sialoregulator nanr from escherichia COLI… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ON4
- Type
- protein
- Length
- 431 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hth-type transcriptional repressor nanr
- UniProt
- P0A8W0
- Ligands
- P4K, SLB, ZN
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 72% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hth-type transcriptional repressor nanr | protein | 217 | 72% helix, 2% strand | P0A8W0 |
| B | Hth-type transcriptional repressor nanr | protein | 214 | 71% helix, 2% strand | P0A8W0 |
Ligands and binding sites
- P4K · polyethylene glycol · ligand · chains A, B
- SLB · N-acetyl-beta-neuraminic acid · sugar · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 681 | 0.81 | 0.85 | 54 | P4K |
| 2 | 479 | 0.77 | 0.85 | 49 | empty |
| 3 | 248 | 0.59 | 0.79 | 27 | empty |
| 4 | 159 | 0.52 | 0.79 | 29 | empty |
| 5 | 137 | 0.49 | 0.79 | 23 | SLB |
Interfaces
1 interface between chains.
- A–B · 2140 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6ON4 · Crystal structure of the GntR-type sialoregulator NanR from Escherichia coli, in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A8W0 · AlphaFold monomer V2.0 prediction for hth-type transcriptional repressor nanr (P0A8W0) · a predicted model of the same protein · chain A against A, TM-score 0.62
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 P0A8W0
- Elsewhere: RCSB PDB 6ON4 · PDBe 6ON4 · UniProt P0A8W0
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