Research workbench
Nv polymerase post-incorporation-like complex
Analyse Nv polymerase post-incorporation-like complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QPX
- Type
- protein + RNA
- Length
- 510 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyprotein; RNA (5'-R(*UP*GP*CP*CP*CP*GP*GP*G)-3'); RNA (5'-R(*U*AP*CP*CP*CP*GP*GP*G)-3')
- EC
- 2.7.7.48
- UniProt
- Q70ET3
- Ligands
- MN
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyprotein (EC 2.7.7.48) | protein | 495 | 42% helix, 17% strand | Q70ET3 |
| P | RNA (5'-R(*UP*GP*CP*CP*CP*GP*GP*G)-3') | rna | 8 | — | — |
| T | RNA (5'-R(*U*AP*CP*CP*CP*GP*GP*G)-3') | rna | 7 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 3 copies · chains A, P
- GOL · Glycerol · additive · 2 copies · chains A, P, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1173 | 0.79 | 0.81 | 87 | GOL |
| 2 | 172 | 0.72 | 0.90 | 33 | empty |
| 3 | 60 | 0.30 | 0.75 | 18 | GOL |
Interfaces
3 interfaces between chains.
- A–P · 951 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–T · 936 Ų buried · 26 hydrogen bonds · protein-nucleic
- P–T · 329 Ų buried · 30 hydrogen bonds · nucleic-nucleic
Compared structures
- 4QPX · NV polymerase post-incorporation-like complex · 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 Q70ET3
- Elsewhere: RCSB PDB 4QPX · PDBe 4QPX · UniProt Q70ET3
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