MolNFT v1 · #184163 · protein + RNA
Nontypeable haemophillus influenzae sapa in open and closed conformations, in complex with double stranded RNA
7OG0 · ABC-type transport system, periplasmic component, involved…: “Nontypeable haemophillus influenzae sapa in open and closed conformations, in complex with double stranded RNA”. X-ray diffraction, 1 ligand (CA), 10 pockets (best…
- 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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