MolNFT v1 · #182403 · protein + RNA
Bartonella henselae nrnc cleaving pgg in the presence of MN2+
7MPQ · Nanornase C: “Bartonella henselae nrnc cleaving pgg in the presence of MN2+”. X-ray diffraction, 2 ligands (5GP, MN), 20 pockets (best druggability 0.79). MolNFT v1 #182403 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7MPQ
- Type
- protein + RNA
- Length
- 1,641 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nanornase C; 5'-phosphorylated gg
- UniProt
- X5MEI1
- Ligands
- 5GP, MN
- Pockets
- 20 · best druggability 0.79
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 |
| C, E, G, I, K | Nanornase C | protein | 205 | 41% helix, 16% strand | X5MEI1 |
| M, O | Nanornase C | protein | 204 | 43% helix, 16% strand | X5MEI1 |
| R | 5'-phosphorylated gg | rna | 2 | — | — |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 14 copies · chains A, E, G, C, I, M, O, K
- MN · Manganese (II) ion · metal · 16 copies · chains A, C, E, G, R, I, K, M, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 963 | 0.79 | 0.81 | 92 | 5GP, MN |
| 2 | 1012 | 0.76 | 0.79 | 94 | 5GP, MN |
| 3 | 726 | 0.76 | 0.81 | 65 | 5GP, MN |
| 4 | 681 | 0.74 | 0.80 | 61 | 5GP, MN |
| 5 | 324 | 0.68 | 0.82 | 39 | 5GP, MN |
Interfaces
19 interfaces between chains.
- E–M · 1287 Ų buried · 8 hydrogen bonds · protein-protein
- A–G · 1263 Ų buried · 8 hydrogen bonds · protein-protein
- C–K · 1260 Ų buried · 8 hydrogen bonds · protein-protein
- I–O · 1241 Ų buried · 8 hydrogen bonds · protein-protein
- G–M · 486 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7MPQ · Bartonella henselae NrnC cleaving pGG in the presence of Mn2+ · 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 7MPQ · PDBe 7MPQ · UniProt X5MEI1
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