Research workbench
Sulfur binding domain and sra domain of scomcra complexed with phosphorothioated DNA
Analyse Sulfur binding domain and sra domain of scomcra complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZMN
- Type
- protein + DNA
- Length
- 344 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein mcra; DNA (5'-D(*CP*CP*CP*GP*(GS)P*CP*CP*GP*GP*G)-3')
- UniProt
- Q9L0M9
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein mcra | protein | 324 | 38% helix, 21% strand | Q9L0M9 |
| B, C | DNA (5'-D(*CP*CP*CP*GP*(GS)P*CP*CP*GP*GP*G)-3') | dna | 10 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 618 | 0.73 | 0.80 | 64 | SO4 |
| 2 | 113 | 0.63 | 0.87 | 20 | empty |
| 3 | 262 | 0.51 | 0.75 | 29 | empty |
| 4 | 72 | 0.39 | 0.79 | 20 | empty |
| 5 | 97 | 0.39 | 0.76 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–C · 491 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–B · 487 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–C · 456 Ų buried · 35 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5ZMN · Sulfur binding domain and SRA 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 5ZMN · PDBe 5ZMN · UniProt Q9L0M9
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