MolNFT v1 · #99479 · protein + RNA
Crystal structure of the aptamer mine-lysozyme complex
4M4O: “Crystal structure of the aptamer mine-lysozyme complex”. X-ray diffraction, 2 ligands (MG, NA), 5 pockets (best druggability 0.47). MolNFT v1 #99479 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4M4O
- Type
- protein + RNA
- Length
- 188 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysozyme C; RNA (59-mer)
- EC
- 3.2.1.17
- UniProt
- P00698
- Ligands
- MG, NA
- Pockets
- 5 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysozyme C (EC 3.2.1.17) | protein | 129 | 40% helix, 11% strand | P00698 |
| B | RNA (59-mer) | rna | 59 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 305 | 0.47 | 0.72 | 20 | empty |
| 2 | 141 | 0.41 | 0.76 | 15 | MG |
| 3 | 102 | 0.38 | 0.75 | 18 | empty |
| 4 | 76 | 0.31 | 0.74 | 16 | empty |
| 5 | 94 | 0.29 | 0.72 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 419 Ų buried · 12 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4M4O · Crystal structure of the aptamer minE-lysozyme 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 P00698
- Elsewhere: RCSB PDB 4M4O · PDBe 4M4O · UniProt P00698
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