MolNFT v1 · #141694 · protein + DNA
Crystal structure of MOSUB1-ssdna complex in phosphate buffer
5ZG9: “Crystal structure of MOSUB1-ssdna complex in phosphate buffer”. X-ray diffraction, 1 ligand (PO4), 2 pockets (best druggability 0.37). MolNFT v1 #141694 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ZG9
- Type
- protein + DNA
- Length
- 177 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MOSUB1; DNA (5'- D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*G)-3')
- UniProt
- L7IX95
- Ligands
- PO4
- Pockets
- 2 · best druggability 0.37
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MOSUB1 | protein | 83 | 24% helix, 46% strand | L7IX95 |
| B | MOSUB1 | protein | 82 | 24% helix, 46% strand | L7IX95 |
| C | DNA (5'- D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*G)-3') | dna | 12 | — | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.37 | 0.76 | 22 | empty |
| 2 | 69 | 0.31 | 0.74 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1670 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 642 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–C · 213 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 5ZG9 · Crystal structure of MoSub1-ssDNA complex in phosphate buffer · 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 L7IX95
- Elsewhere: RCSB PDB 5ZG9 · PDBe 5ZG9 · UniProt L7IX95
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