MolNFT v1 · #156240 · protein
Crystal structure of C-terminal DNA-binding domain of escherichia COLI ompr as a domain-swapped dimer
6LXM · Transcriptional regulatory protein ompr: “Crystal structure of C-terminal DNA-binding domain of escherichia COLI ompr as a domain-swapped dimer”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.47). MolNFT v1…
- PDB
- 6LXM
- Type
- protein
- Length
- 302 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulatory protein ompr
- UniProt
- A0A376JR14
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, B | Transcriptional regulatory protein ompr | protein | 101 | 42% helix, 22% strand | A0A376JR14 |
| A | Transcriptional regulatory protein ompr | protein | 100 | 40% helix, 23% strand | A0A376JR14 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains C, A, B
- GOL · Glycerol · additive · 9 copies · chains C, A, B
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.47 | 0.78 | 16 | GOL |
| 2 | 90 | 0.31 | 0.72 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2427 Ų buried · 24 hydrogen bonds · protein-protein
- C–B · 141 Ų buried · 1 hydrogen bond · protein-protein
- C–A · 35 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6LXM · Crystal structure of C-terminal DNA-binding domain of Escherichia coli OmpR as a… · the same entry in another collection · chain C against C, 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 A0A376JR14
- Elsewhere: RCSB PDB 6LXM · PDBe 6LXM · UniProt A0A376JR14
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