Research workbench
Nontypeable haemophillus influenzae sapa in open and closed conformations, in complex with double stranded RNA
Analyse Nontypeable haemophillus influenzae sapa in open and closed conformations, in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OG0
- Type
- protein + RNA
- Length
- 1,029 residues
- Chains
- 4
- 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
- CA
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ABC-type transport system, periplasmic component, involved in antimicrobial peptide resistance | protein | 497 | 30% helix, 24% strand | Q4QL73 |
| B | ABC-type transport system, periplasmic component, involved in antimicrobial peptide resistance | protein | 498 | 31% helix, 24% strand | Q4QL73 |
| D, E | 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 | 17 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 343 | 0.72 | 0.84 | 41 | empty |
| 2 | 282 | 0.71 | 0.86 | 40 | empty |
| 3 | 262 | 0.63 | 0.81 | 34 | empty |
| 4 | 146 | 0.58 | 0.83 | 35 | empty |
| 5 | 179 | 0.55 | 0.79 | 32 | empty |
Interfaces
3 interfaces between chains.
- A–B · 607 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 217 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–D · 209 Ų buried · 5 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7OG0 · Nontypeable Haemophillus influenzae SapA in open and closed conformations, in complex… · 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 7OG0 · PDBe 7OG0 · UniProt Q4QL73
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