MolNFT v1 · #182399 · protein + RNA
Bartonella henselae nrnc bound to paa
7MPM · Nanornase C: “Bartonella henselae nrnc bound to paa”. X-ray diffraction, 20 pockets (best druggability 0.74). MolNFT v1 #182399 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7MPM
- Type
- protein + RNA
- Length
- 1,654 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nanornase C; 5'-phosphorylated aa
- UniProt
- X5MEI1
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 42% 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 aa | rna | 2 | — | — |
| C, E, G, K | Nanornase C | protein | 205 | 41% helix, 16% strand | X5MEI1 |
| I, M, O | Nanornase C | protein | 204 | 43% 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 | 967 | 0.74 | 0.78 | 88 | empty |
| 2 | 816 | 0.73 | 0.78 | 68 | empty |
| 3 | 788 | 0.73 | 0.78 | 67 | empty |
| 4 | 785 | 0.73 | 0.78 | 65 | empty |
| 5 | 155 | 0.45 | 0.76 | 22 | empty |
Interfaces
40 interfaces between chains.
- E–M · 1286 Ų buried · 8 hydrogen bonds · protein-protein
- A–G · 1278 Ų buried · 8 hydrogen bonds · protein-protein
- I–O · 1276 Ų buried · 8 hydrogen bonds · protein-protein
- C–K · 1271 Ų buried · 8 hydrogen bonds · protein-protein
- E–I · 473 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7MPM · Bartonella henselae NrnC bound to pAA · 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 7MPM · PDBe 7MPM · UniProt X5MEI1
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