Research workbench
Nontypeable haemophillus influenzae sapa in complex with double stranded RNA
Analyse Nontypeable haemophillus influenzae sapa in complex with double stranded RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OFZ
- Type
- protein + RNA
- Length
- 516 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC-type transport system, periplasmic component, involved in antimicrobial peptide…
- UniProt
- Q4QL73
- Ligands
- NA
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ABC-type transport system, periplasmic component, involved in antimicrobial peptide resistance | protein | 497 | 27% helix, 23% strand | Q4QL73 |
| C | RNA (5'- R(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3') | rna | 19 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 182 | 0.81 | 0.95 | 38 | empty |
| 2 | 272 | 0.72 | 0.86 | 51 | empty |
| 3 | 81 | 0.56 | 0.86 | 22 | empty |
| 4 | 172 | 0.52 | 0.78 | 25 | empty |
| 5 | 87 | 0.38 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–C · 228 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7OFZ · Nontypeable Haemophillus influenzae SapA in complex with double stranded RNA · 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 Q4QL73
- Elsewhere: RCSB PDB 7OFZ · PDBe 7OFZ · UniProt Q4QL73
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