MolNFT v1 · #74047 · protein + RNA
Poliovirus polymerase elongation complex with 3'-deoxy-CTP
3OL9: “Poliovirus polymerase elongation complex with 3'-deoxy-CTP”. X-ray diffraction, 2 ligands (POP, ZN), 20 pockets (best druggability 0.83). MolNFT v1 #74047 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3OL9
- Type
- protein + RNA
- Length
- 1,988 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase; RNA (5'- R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*CP*GP*…
- EC
- 2.7.7.48
- UniProt
- B3VQP5
- Ligands
- POP, ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I, M | Polymerase (EC 2.7.7.48) | protein | 461 | 41% helix, 15% strand | B3VQP5 |
| B, F | RNA (5'- R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*CP*GP* GP*AP*AP*A)-3') | rna | 17 | — | — |
| C, G, K, O | RNA (5'-R(*GP*CP*CP*CP*GP*GP*AP*CP*GP*AP*GP*AP*GP*AP*(O2C) )-3') | rna | 15 | — | — |
| D, H | RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3') | rna | 3 | — | — |
| J, N | RNA (5'- R(*AP*AP*GP*UP*CP*UP*CP*CP*AP*GP*GP*UP*CP*UP*CP*UP*CP*GP*UP*CP*CP*GP* GP*AP*AP*A)-3') | rna | 18 | — | — |
| L, P | RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3') | rna | 4 | — | — |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 4 copies · chains A, C, E, G, I, K, M, O
- ZN · Zinc ion · metal · 4 copies · chains A, E, I, M
- IPA · Isopropyl alcohol · additive · 15 copies · chains A, C, E, I, K, M, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1167 | 0.83 | 0.85 | 102 | POP |
| 2 | 866 | 0.81 | 0.84 | 56 | IPA |
| 3 | 847 | 0.81 | 0.84 | 51 | IPA |
| 4 | 808 | 0.81 | 0.84 | 56 | POP, IPA |
| 5 | 81 | 0.73 | 0.97 | 21 | empty |
Interfaces
27 interfaces between chains.
- E–F · 1247 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–B · 1245 Ų buried · 17 hydrogen bonds · protein-nucleic
- M–N · 1239 Ų buried · 18 hydrogen bonds · protein-nucleic
- I–J · 1239 Ų buried · 18 hydrogen bonds · protein-nucleic
- M–O · 889 Ų buried · 12 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 3OL9 · Poliovirus polymerase elongation complex with 3'-deoxy-CTP · 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 B3VQP5
- Elsewhere: RCSB PDB 3OL9 · PDBe 3OL9 · UniProt B3VQP5
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