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Crystal structure of macro domain of venezuelan equine encephalitis virus in complex with ADP-ribose
Analyse Crystal structure of macro domain of venezuelan equine encephalitis virus in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GQO
- Type
- protein
- Length
- 640 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 3
- UniProt
- P36328
- Ligands
- APR
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-structural protein 3 | protein | 161 | 38% helix, 20% strand | P36328 |
| B | Non-structural protein 3 | protein | 159 | 38% helix, 21% strand | P36328 |
| C, D | Non-structural protein 3 | protein | 160 | 39% helix, 20% strand | P36328 |
Ligands and binding sites
- APR · Adenosine-5-diphosphoribose · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1058 | 0.75 | 0.78 | 79 | empty |
| 2 | 210 | 0.62 | 0.82 | 29 | APR |
| 3 | 217 | 0.60 | 0.81 | 32 | APR |
| 4 | 203 | 0.59 | 0.81 | 28 | APR |
| 5 | 191 | 0.57 | 0.80 | 28 | APR |
Interfaces
4 interfaces between chains.
- C–D · 339 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 326 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 261 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 157 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3GQO · Crystal structure of macro domain of Venezuelan Equine Encephalitis virus in complex with… · 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 P36328
- Elsewhere: RCSB PDB 3GQO · PDBe 3GQO · UniProt P36328
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