MolNFT v1 · #141894 · protein + DNA
Sulfur binding domain of scomcra complexed with phosphorothioated DNA
5ZMO · Uncharacterized protein mcra: “Sulfur binding domain of scomcra complexed with phosphorothioated DNA”. X-ray diffraction, 1 ligand (PO4), 2 pockets (best druggability 0.50). MolNFT v1 #141894 on GenesisL1: 3D structure, binding…
- PDB
- 5ZMO
- Type
- protein + DNA
- Length
- 172 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein mcra; DNA (5'-D(P*CP*CP*GP*(GS)P*CP*CP*GP*G)-3')
- UniProt
- Q9L0M9
- Ligands
- PO4
- Pockets
- 2 · best druggability 0.50
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein mcra | protein | 158 | 54% helix, 10% strand | Q9L0M9 |
| B | DNA (5'-D(P*CP*CP*GP*(GS)P*CP*CP*GP*G)-3') | dna | 7 | — | — |
| C | DNA (5'-D(P*CP*CP*GP*(GS)P*CP*CP*GP*G)-3') | dna | 7 | — | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 3 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 108 | 0.50 | 0.82 | 18 | empty |
| 2 | 85 | 0.38 | 0.77 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 522 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–C · 383 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–C · 352 Ų buried · 33 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5ZMO · Sulfur binding domain of ScoMcrA complexed with phosphorothioated DNA · 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 Q9L0M9
- Elsewhere: RCSB PDB 5ZMO · PDBe 5ZMO · UniProt Q9L0M9
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