Research workbench
Poliovirus polymerase elongation complex with 2'-deoxy-CTP
Analyse Poliovirus polymerase elongation complex with 2'-deoxy-CTP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OLA
- Type
- protein + RNA
- Length
- 1,986 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
- DCP, ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 7 distinct chains · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I, M | Polymerase (EC 2.7.7.48) | protein | 461 | 41% helix, 14% 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 | DNA/RNA (5'-R(*GP*CP*CP*CP*GP*GP*AP*CP*GP*AP*GP*AP*GP*A)- D(P*C)-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 | — | — |
| K, O | RNA (5'-R(*GP*CP*CP*CP*GP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3') | rna | 14 | — | — |
| L, P | RNA (5'-R(*GP*GP*GP*AP*GP*AP*UP*GP*A)-3') | rna | 4 | — | — |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · 2 copies · chains I, J, K, M, N, O
- ZN · Zinc ion · metal · 4 copies · chains A, E, I, M
- IPA · Isopropyl alcohol · additive · 10 copies · chains A, E, I, L, M
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, C, I, K
- GOL · Glycerol · additive · 2 copies · chains A, I
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 | 1152 | 0.83 | 0.84 | 87 | PEG, DCP |
| 2 | 886 | 0.81 | 0.84 | 53 | PEG |
| 3 | 812 | 0.80 | 0.84 | 57 | empty |
| 4 | 777 | 0.80 | 0.84 | 57 | empty |
| 5 | 399 | 0.77 | 0.86 | 67 | empty |
Interfaces
27 interfaces between chains.
- I–J · 1246 Ų buried · 20 hydrogen bonds · protein-nucleic
- M–N · 1246 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–B · 1245 Ų buried · 17 hydrogen bonds · protein-nucleic
- E–F · 1242 Ų buried · 17 hydrogen bonds · protein-nucleic
- E–G · 873 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 3OLA · Poliovirus polymerase elongation complex with 2'-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 3OLA · PDBe 3OLA · UniProt B3VQP5
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