MolNFT v1 · #110758 · protein
Structure of a lipoprotein from streptococcus agalactiae
4Y68 · Putative nisin-resistance protein: “Structure of a lipoprotein from streptococcus agalactiae”. X-ray diffraction, 10 pockets (best druggability 0.76). MolNFT v1 #110758 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4Y68
- Type
- protein
- Length
- 1,147 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative nisin-resistance protein
- UniProt
- Q3DLX7
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A, D | Putative nisin-resistance protein | protein | 287 | 37% helix, 23% strand | Q3DLX7 |
| B | Putative nisin-resistance protein | protein | 286 | 36% helix, 23% strand | Q3DLX7 |
Ligands and binding sites
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains C, D, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 624 | 0.76 | 0.82 | 77 | MES |
| 2 | 798 | 0.74 | 0.79 | 73 | empty |
| 3 | 770 | 0.71 | 0.77 | 66 | empty |
| 4 | 699 | 0.70 | 0.77 | 85 | empty |
| 5 | 609 | 0.69 | 0.78 | 79 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1924 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1723 Ų buried · 19 hydrogen bonds · protein-protein
- C–A · 792 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 753 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4Y68 · Structure of a lipoprotein from Streptococcus agalactiae · 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 Q3DLX7
- Elsewhere: RCSB PDB 4Y68 · PDBe 4Y68 · UniProt Q3DLX7
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