MolNFT v1 · #140320 · protein + RNA
Crystal structure of the coxsackievirus A16 polymerase elongation complex
5Y6Z · Genome polyprotein: “Crystal structure of the coxsackievirus A16 polymerase elongation complex”. X-ray diffraction, 2 ligands (MG, PO4), 15 pockets (best druggability 0.82). MolNFT v1 #140320 on GenesisL1: 3D structure, binding…
- PDB
- 5Y6Z
- Type
- protein + RNA
- Length
- 973 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein; Template RNA (33-mer); Product RNA (14-mer)
- UniProt
- L7WS61
- Ligands
- MG, PO4
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome polyprotein | protein | 457 | 43% helix, 16% strand | L7WS61 |
| B | Template RNA (33-mer) | rna | 15 | — | — |
| C, G | Product RNA (14-mer) | rna | 12 | — | — |
| E | Genome polyprotein | protein | 460 | 42% helix, 15% strand | L7WS61 |
| F | Template RNA (33-mer) | rna | 17 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains E, G
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, G
- GOL · Glycerol · additive · 6 copies · chains A, B, C, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.82 | 0.84 | 86 | PO4, GOL |
| 2 | 609 | 0.77 | 0.84 | 49 | PO4 |
| 3 | 93 | 0.74 | 0.96 | 22 | empty |
| 4 | 269 | 0.71 | 0.86 | 30 | GOL |
| 5 | 189 | 0.70 | 0.88 | 31 | empty |
Interfaces
9 interfaces between chains.
- E–F · 1224 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–B · 1188 Ų buried · 22 hydrogen bonds · protein-nucleic
- E–G · 697 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–C · 694 Ų buried · 11 hydrogen bonds · protein-nucleic
- F–G · 593 Ų buried · 56 hydrogen bonds · nucleic-nucleic
Compared structures
- 5Y6Z · Crystal structure of the coxsackievirus A16 polymerase elongation complex · 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 L7WS61
- Elsewhere: RCSB PDB 5Y6Z · PDBe 5Y6Z · UniProt L7WS61
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