MolNFT v1 · #162160 · protein
Getah virus macro domain in complex with adpr in double open conformation
6R0P · Non-structural polyprotein: “Getah virus macro domain in complex with adpr in double open conformation”. X-ray diffraction, 1 ligand (JNT), 3 pockets (best druggability 0.63). MolNFT v1 #162160 on GenesisL1: 3D structure, binding…
- PDB
- 6R0P
- Type
- protein
- Length
- 320 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural polyprotein
- UniProt
- A0A143SL92
- Ligands
- JNT
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-structural polyprotein | protein | 159 | 38% helix, 21% strand | A0A143SL92 |
| B | Non-structural polyprotein | protein | 161 | 36% helix, 21% strand | A0A143SL92 |
Ligands and binding sites
- JNT · [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-2,3,4,5-tetrakis(oxidanyl)pentyl] hydrogen phosphate · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 205 | 0.63 | 0.83 | 27 | JNT |
| 2 | 190 | 0.59 | 0.81 | 30 | JNT |
| 3 | 258 | 0.57 | 0.78 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 363 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6R0P · Getah virus macro domain in complex with ADPr in double open conformation · 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 A0A143SL92
- Elsewhere: RCSB PDB 6R0P · PDBe 6R0P · UniProt A0A143SL92
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