MolNFT v1 · #156629 · protein
Native bbvci B2 dimer in space group C222
6MAG · Bbvci endonuclease subunit 2: “Native bbvci B2 dimer in space group C222”. X-ray diffraction, 1 ligand (PO4), 13 pockets (best druggability 0.60). MolNFT v1 #156629 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6MAG
- Type
- protein
- Length
- 846 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bbvci endonuclease subunit 2
- UniProt
- Q5D6Y4
- Ligands
- PO4
- Pockets
- 13 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Bbvci endonuclease subunit 2 | protein | 282 | 44% helix, 24% strand | Q5D6Y4 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 22 copies · chains A, B, C
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 488 | 0.60 | 0.74 | 48 | empty |
| 2 | 466 | 0.58 | 0.74 | 44 | empty |
| 3 | 221 | 0.49 | 0.75 | 23 | PO4 |
| 4 | 177 | 0.46 | 0.75 | 22 | PO4 |
| 5 | 188 | 0.45 | 0.74 | 22 | PO4 |
Interfaces
3 interfaces between chains.
- B–C · 297 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 230 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 164 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6MAG · native BbvCI B2 dimer in space group C222 · 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 Q5D6Y4
- Elsewhere: RCSB PDB 6MAG · PDBe 6MAG · UniProt Q5D6Y4
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