MolNFT v1 · #98837 · protein + DNA
Crystal structure of S. aureus mepr-DNA complex
4LLL: “Crystal structure of S. aureus mepr-DNA complex”. X-ray diffraction, 20 pockets (best druggability 0.84). MolNFT v1 #98837 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4LLL
- Type
- protein + DNA
- Length
- 1,229 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mepr; Palindromized mepr operator sequence
- UniProt
- Q5Y812
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 71% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, J | Mepr | protein | 138 | 69% helix, 8% strand | Q5Y812 |
| D, I | Mepr | protein | 137 | 72% helix, 8% strand | Q5Y812 |
| M | Mepr | protein | 124 | 68% helix, 9% strand | Q5Y812 |
| O | Mepr | protein | 135 | 73% helix, 7% strand | Q5Y812 |
| E, F, G, H, K, L | Palindromized mepr operator sequence | dna | 24 | — | — |
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1134 | 0.84 | 0.85 | 116 | empty |
| 2 | 1151 | 0.83 | 0.84 | 113 | empty |
| 3 | 988 | 0.81 | 0.83 | 72 | empty |
| 4 | 191 | 0.70 | 0.87 | 32 | empty |
| 5 | 436 | 0.66 | 0.78 | 47 | empty |
Interfaces
20 interfaces between chains.
- A–B · 2169 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 2039 Ų buried · 11 hydrogen bonds · protein-protein
- I–J · 1811 Ų buried · 17 hydrogen bonds · protein-protein
- K–L · 1022 Ų buried · 101 hydrogen bonds · nucleic-nucleic
- G–H · 1014 Ų buried · 105 hydrogen bonds · nucleic-nucleic
Compared structures
- 4LLL · Crystal structure of S. aureus MepR-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 Q5Y812
- Elsewhere: RCSB PDB 4LLL · PDBe 4LLL · UniProt Q5Y812
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