Research workbench
Poliovirus polymerase elongation complex with CTP
Analyse Poliovirus polymerase elongation complex with CTP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OL7
- Type
- protein + RNA
- Length
- 1,984 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, MG, ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I, M | Polymerase (EC 2.7.7.48) | protein | 461 | 42% 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*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 | 16 | — | — |
| 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
- MG · Magnesium ion · metal · 6 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, E, I, M, N, O
- GOL · Glycerol · additive · 8 copies · chains E, I, J, K, M, N, O
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, E, J, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1159 | 0.83 | 0.85 | 93 | MG, POP |
| 2 | 952 | 0.83 | 0.85 | 69 | MG, POP |
| 3 | 1079 | 0.83 | 0.84 | 90 | MG, POP |
| 4 | 1186 | 0.81 | 0.83 | 79 | POP |
| 5 | 104 | 0.75 | 0.96 | 21 | empty |
Interfaces
27 interfaces between chains.
- I–J · 1247 Ų buried · 13 hydrogen bonds · protein-nucleic
- M–N · 1241 Ų buried · 15 hydrogen bonds · protein-nucleic
- E–F · 1224 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–B · 1222 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–C · 932 Ų buried · 15 hydrogen bonds · protein-nucleic
Compared structures
- 3OL7 · Poliovirus polymerase elongation complex with 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 3OL7 · PDBe 3OL7 · UniProt B3VQP5
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