Research workbench
Poliovirus polymerase elongation complex (R4_FORM)
Analyse Poliovirus polymerase elongation complex (R4_FORM) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K4T
- Type
- protein + RNA
- Length
- 990 residues
- Chains
- 8
- 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
- ZN
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 43% 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 | 43% 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*GP*GP*AP*AP*A)- 3') | rna | 17 | — | — |
| C, G | RNA (5'-R(P*UP*GP*UP*UP*CP*CP*GP*AP*GP*AP*GP*A)-3') | rna | 12 | — | — |
| D, H | RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3') | rna | 4 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, E
- GOL · Glycerol · additive · 4 copies · chains A, B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1085 | 0.83 | 0.85 | 68 | empty |
| 2 | 681 | 0.82 | 0.87 | 72 | empty |
| 3 | 124 | 0.73 | 0.93 | 28 | empty |
| 4 | 243 | 0.72 | 0.87 | 29 | empty |
| 5 | 115 | 0.70 | 0.92 | 24 | GOL |
Interfaces
14 interfaces between chains.
- A–B · 1231 Ų buried · 19 hydrogen bonds · protein-nucleic
- E–F · 1224 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–C · 781 Ų buried · 9 hydrogen bonds · protein-nucleic
- E–G · 778 Ų buried · 9 hydrogen bonds · protein-nucleic
- F–G · 503 Ų buried · 46 hydrogen bonds · nucleic-nucleic
Compared structures
- 4K4T · Poliovirus polymerase elongation complex (r4_form) · 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 P03300
- Elsewhere: RCSB PDB 4K4T · PDBe 4K4T · UniProt P03300
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