MolNFT v1 · #155093 · protein + RNA
Crystal structure of enterovirus 71 polymerase elongation complex (ddctp form)
6KWR · RNA-dependent RNA polymerase: “Crystal structure of enterovirus 71 polymerase elongation complex (ddctp form)”. X-ray diffraction, 3 ligands (DCT, MG, ZN), 6 pockets (best druggability 0.81). MolNFT v1 #155093 on GenesisL1: 3D…
- PDB
- 6KWR
- Type
- protein + RNA
- Length
- 488 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-dependent RNA polymerase; RNA (31-mer); RNA…
- EC
- 2.7.7.48
- UniProt
- A0A023RBB6
- Ligands
- DCT, MG, ZN
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-dependent RNA polymerase (EC 2.7.7.48) | protein | 453 | 43% helix, 16% strand | A0A023RBB6 |
| B | RNA (31-mer) | rna | 28 | — | — |
| C | RNA (5'-R(*UP*GP*UP*UP*CP*CP*GP*AP*GP*AP*GP*A)-D(P*(DOC))- 3') | rna | 7 | — | — |
Ligands and binding sites
- DCT · 2',3'-dideoxycytidine 5'-triphosphate · ligand · chains A, B, C
- MG · Magnesium ion · metal · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1024 | 0.81 | 0.83 | 75 | DCT |
| 2 | 164 | 0.70 | 0.89 | 27 | empty |
| 3 | 217 | 0.49 | 0.76 | 27 | empty |
| 4 | 55 | 0.45 | 0.84 | 11 | empty |
| 5 | 115 | 0.42 | 0.77 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1517 Ų buried · 35 hydrogen bonds · protein-nucleic
- A–C · 593 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–C · 367 Ų buried · 35 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6KWR · Crystal structure of enterovirus 71 polymerase elongation complex (ddCTP 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 A0A023RBB6
- Elsewhere: RCSB PDB 6KWR · PDBe 6KWR · UniProt A0A023RBB6
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