Research workbench
Bartonella henselae NrnC bound to pGG
Analyse Bartonella henselae NrnC bound to pGG in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MPL
- Type
- protein + RNA
- Length
- 1,655 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Bartonella henselae; SYNTHETIC CONSTRUCT
- Molecule
- NanoRNase C; 5'-phosphorylated GG
- UniProt
- X5MEI1
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · resolution 1.8 · 4 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NanoRNase C | protein | 206 | 41% helix, 16% strand | X5MEI1 |
| B, D, F, H, J, L, N, P | 5'-phosphorylated GG | rna | 2 | — | — |
| C, E, G, I, K | NanoRNase C | protein | 205 | 41% helix, 16% strand | X5MEI1 |
| M, O | NanoRNase C | protein | 204 | 40% helix, 16% strand | X5MEI1 |
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 903 | 0.75 | 0.79 | 89 | empty |
| 2 | 918 | 0.75 | 0.78 | 83 | empty |
| 3 | 885 | 0.75 | 0.79 | 84 | empty |
| 4 | 739 | 0.74 | 0.80 | 69 | empty |
| 5 | 153 | 0.45 | 0.76 | 22 | empty |
Interfaces
40 interfaces between chains.
- C–K · 1276 Ų buried · 8 hydrogen bonds · protein-protein
- E–M · 1264 Ų buried · 8 hydrogen bonds · protein-protein
- A–G · 1263 Ų buried · 8 hydrogen bonds · protein-protein
- I–O · 1244 Ų buried · 8 hydrogen bonds · protein-protein
- G–M · 483 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7MPL · Bartonella henselae nrnc bound to pgg · 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 X5MEI1
- Elsewhere: RCSB PDB 7MPL · PDBe 7MPL · UniProt X5MEI1
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