MolNFT v1 · #100308 · protein
Rdrp from japanesese encephalitis virus
4MTP · RNA dependent RNA polymerase: “Rdrp from japanesese encephalitis virus”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.86). MolNFT v1 #100308 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4MTP
- Type
- protein
- Length
- 2,313 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA dependent RNA polymerase
- EC
- 2.7.7.48
- UniProt
- G3LHD9
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA dependent RNA polymerase (EC 2.7.7.48) | protein | 591 | 47% helix, 12% strand | G3LHD9 |
| C | RNA dependent RNA polymerase (EC 2.7.7.48) | protein | 585 | 47% helix, 12% strand | G3LHD9 |
| D | RNA dependent RNA polymerase (EC 2.7.7.48) | protein | 546 | 51% helix, 7% strand | G3LHD9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 904 | 0.86 | 0.88 | 103 | empty |
| 2 | 969 | 0.82 | 0.83 | 97 | empty |
| 3 | 1074 | 0.79 | 0.81 | 105 | ZN |
| 4 | 749 | 0.77 | 0.81 | 60 | empty |
| 5 | 483 | 0.72 | 0.81 | 62 | empty |
Interfaces
6 interfaces between chains.
- A–B · 750 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 505 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 478 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 437 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 422 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4MTP · RdRp from Japanesese Encephalitis Virus · the same entry in another collection · chain B against B, 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 G3LHD9
- Elsewhere: RCSB PDB 4MTP · PDBe 4MTP · UniProt G3LHD9
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