MolNFT v1 · #97139 · protein + RNA
Poliovirus polymerase elongation complex (R5+1_FORM)
4K4V · RNA-directed RNA polymerase 3D-pol: “Poliovirus polymerase elongation complex (R5+1_FORM)”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.84). MolNFT v1 #97139 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4K4V
- Type
- protein + RNA
- Length
- 970 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase 3D-pol; RNA (5'- R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*…
- EC
- 2.7.7.48
- UniProt
- P03300
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | RNA-directed RNA polymerase 3D-pol (EC 2.7.7.48) | protein | 462 | 42% helix, 15% strand | P03300 |
| B, F | RNA (5'- R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*UP*CP*GP*UP*CP* GP*AP*AP*A)-3') | rna | 13 | — | — |
| C, G | DNA/RNA (5'- R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*GP*A)-D(P*C)-3') | rna | 10 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1174 | 0.84 | 0.85 | 101 | empty |
| 2 | 1181 | 0.83 | 0.85 | 96 | empty |
| 3 | 200 | 0.70 | 0.88 | 31 | empty |
| 4 | 184 | 0.70 | 0.88 | 32 | empty |
Interfaces
6 interfaces between chains.
- E–F · 1086 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–B · 1070 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–C · 736 Ų buried · 9 hydrogen bonds · protein-nucleic
- E–G · 731 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–C · 480 Ų buried · 45 hydrogen bonds · nucleic-nucleic
Compared structures
- 4K4V · Poliovirus polymerase elongation complex (r5+1_form) · the same entry in another collection · chain E against E, 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 P03300
- Elsewhere: RCSB PDB 4K4V · PDBe 4K4V · UniProt P03300
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