Research workbench
Bartonella henselae NrnC complexed with pAGG. D4 symmetry.
Analyse Bartonella henselae NrnC complexed with pAGG. D4 symmetry. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MQD
- Type
- protein + RNA
- Length
- 1,608 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.25
- Source
- Bartonella henselae; SYNTHETIC CONSTRUCT
- Molecule
- NanoRNase C; RNA (5'-R(P*AP*GP*G)-3')
- UniProt
- X5MEI1
- Pockets
- 20 · best druggability 0.68
Structure
electron microscopy · resolution 3.25 · 2 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O | NanoRNase C | protein | 199 | 41% helix, 16% strand | X5MEI1 |
| B, D, F, H, J, L, N, P | RNA (5'-R(P*AP*GP*G)-3') | rna | 2 | — | — |
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 | 431 | 0.68 | 0.80 | 56 | empty |
| 2 | 584 | 0.68 | 0.77 | 61 | empty |
| 3 | 428 | 0.67 | 0.80 | 50 | empty |
| 4 | 470 | 0.67 | 0.79 | 57 | empty |
| 5 | 63 | 0.47 | 0.84 | 19 | empty |
Interfaces
40 interfaces between chains.
- E–I · 1208 Ų buried · 7 hydrogen bonds · protein-protein
- A–M · 1207 Ų buried · 7 hydrogen bonds · protein-protein
- G–O · 1206 Ų buried · 7 hydrogen bonds · protein-protein
- C–K · 1198 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 394 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 7MQD · Bartonella henselae nrnc complexed with pagg. D4 symmetry. · 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 7MQD · PDBe 7MQD · UniProt X5MEI1
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