MolNFT v1 · #176025 · protein + DNA
Crystal structure of full-length cbnr complexed with the target DNA complex
7D98 · Lysr-type regulatory protein: “Crystal structure of full-length cbnr complexed with the target DNA complex”. X-ray diffraction, 20 pockets (best druggability 0.69). MolNFT v1 #176025 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7D98
- Type
- protein + DNA
- Length
- 1,201 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysr-type regulatory protein; DNA (56-mer)
- UniProt
- Q9WXC7
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 6 distinct chains · 45% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysr-type regulatory protein | protein | 285 | 45% helix, 23% strand | Q9WXC7 |
| B | Lysr-type regulatory protein | protein | 283 | 44% helix, 21% strand | Q9WXC7 |
| P | Lysr-type regulatory protein | protein | 288 | 45% helix, 24% strand | Q9WXC7 |
| Q | Lysr-type regulatory protein | protein | 288 | 47% helix, 24% strand | Q9WXC7 |
| G | DNA (56-mer) | dna | 33 | — | — |
| H | DNA (56-mer) | dna | 24 | — | — |
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 267 | 0.69 | 0.84 | 46 | empty |
| 2 | 406 | 0.63 | 0.77 | 32 | empty |
| 3 | 275 | 0.63 | 0.80 | 41 | empty |
| 4 | 346 | 0.56 | 0.75 | 37 | empty |
| 5 | 320 | 0.54 | 0.74 | 47 | empty |
Interfaces
13 interfaces between chains.
- B–P · 1254 Ų buried · 3 hydrogen bonds · protein-protein
- A–Q · 1227 Ų buried · 5 hydrogen bonds · protein-protein
- G–H · 1131 Ų buried · 87 hydrogen bonds · nucleic-nucleic
- P–Q · 1087 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 974 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7D98 · Crystal structure of full-length CbnR complexed with the target DNA complex · 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 Q9WXC7
- Elsewhere: RCSB PDB 7D98 · PDBe 7D98 · UniProt Q9WXC7
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