Research workbench
Bartonella henselae nrnc cleaving pgg in the presence of MG2+
Analyse Bartonella henselae nrnc cleaving pgg in the presence of MG2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MPP
- Type
- protein
- Length
- 1,641 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nanornase C
- UniProt
- X5MEI1
- Ligands
- 5GP, MG
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nanornase C | protein | 206 | 40% helix, 16% strand | X5MEI1 |
| C, E, G, I, K, M, O | Nanornase C | protein | 205 | 41% helix, 16% strand | X5MEI1 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 16 copies · chains A, E, G, C, K, I, M, O
- MG · Magnesium ion · metal · 16 copies · chains A, C, E, G, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 995 | 0.80 | 0.81 | 102 | 5GP, MG |
| 2 | 1006 | 0.80 | 0.81 | 90 | 5GP, MG |
| 3 | 1026 | 0.80 | 0.81 | 95 | 5GP, MG |
| 4 | 1028 | 0.79 | 0.81 | 91 | 5GP, MG |
| 5 | 135 | 0.45 | 0.76 | 21 | empty |
Interfaces
16 interfaces between chains.
- I–O · 1268 Ų buried · 9 hydrogen bonds · protein-protein
- E–M · 1265 Ų buried · 8 hydrogen bonds · protein-protein
- C–K · 1261 Ų buried · 8 hydrogen bonds · protein-protein
- A–G · 1261 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 496 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7MPP · Bartonella henselae NrnC cleaving pGG in the presence of Mg2+ · 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 7MPP · PDBe 7MPP · UniProt X5MEI1
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