MolNFT v1 · #156241 · protein + DNA
Crystal structure of C-terminal DNA-binding domain of escherichia COLI ompr in complex with F1-DNA
6LXN · DNA (27-mer): “Crystal structure of C-terminal DNA-binding domain of escherichia COLI ompr in complex with F1-DNA”. X-ray diffraction, 1 ligand (SO4), 7 pockets (best druggability 0.68). MolNFT v1 #156241 on GenesisL1: 3D structure…
- PDB
- 6LXN
- Type
- protein + DNA
- Length
- 265 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (27-mer); Transcriptional regulatory protein ompr
- UniProt
- A0A376JR14
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (27-mer) | dna | 27 | — | — |
| D | DNA (27-mer) | dna | 27 | — | — |
| A | Transcriptional regulatory protein ompr | protein | 110 | 28% helix, 21% strand | A0A376JR14 |
| B | Transcriptional regulatory protein ompr | protein | 101 | 31% helix, 26% strand | A0A376JR14 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 389 | 0.68 | 0.81 | 35 | empty |
| 2 | 109 | 0.46 | 0.79 | 16 | empty |
| 3 | 181 | 0.45 | 0.75 | 24 | SO4 |
| 4 | 100 | 0.38 | 0.76 | 15 | empty |
| 5 | 82 | 0.36 | 0.77 | 15 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1191 Ų buried · 97 hydrogen bonds · nucleic-nucleic
- C–A · 478 Ų buried · 5 hydrogen bonds · protein-nucleic
- D–A · 474 Ų buried · 13 hydrogen bonds · protein-nucleic
- D–B · 472 Ų buried · 13 hydrogen bonds · protein-nucleic
- C–B · 469 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 6LXN · Crystal structure of C-terminal DNA-binding domain of Escherichia coli OmpR in complex… · 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 6LXN · PDBe 6LXN · UniProt A0A376JR14
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