MolNFT v1 · #164101 · protein
Crystal structure of antirestriction ardc protein from R388 plasmid. MN(II)-bound structure.
6SNA: “Crystal structure of antirestriction ardc protein from R388 plasmid. MN(II)-bound structure.”. X-ray diffraction, 1 ligand (MN), 20 pockets (best druggability 0.86). MolNFT v1 #164101 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6SNA
- Type
- protein
- Length
- 2,008 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ardc protein
- UniProt
- Q6I6B2
- Ligands
- MN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, G, K | Ardc protein | protein | 265 | 46% helix, 15% strand | Q6I6B2 |
| F, J, N, X | Ardc protein | protein | 237 | 44% helix, 16% strand | Q6I6B2 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, F, G, J, K, N, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1007 | 0.86 | 0.86 | 94 | empty |
| 2 | 897 | 0.85 | 0.87 | 90 | empty |
| 3 | 1050 | 0.82 | 0.83 | 86 | empty |
| 4 | 1158 | 0.81 | 0.82 | 83 | empty |
| 5 | 884 | 0.77 | 0.80 | 84 | empty |
Interfaces
8 interfaces between chains.
- B–F · 1984 Ų buried · 17 hydrogen bonds · protein-protein
- K–N · 1983 Ų buried · 9 hydrogen bonds · protein-protein
- A–X · 1933 Ų buried · 9 hydrogen bonds · protein-protein
- G–J · 1929 Ų buried · 9 hydrogen bonds · protein-protein
- B–G · 673 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6SNA · Crystal structure of Antirestriction ArdC protein from R388 plasmid. Mn(II)-bound… · 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 Q6I6B2
- Elsewhere: RCSB PDB 6SNA · PDBe 6SNA · UniProt Q6I6B2
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