MolNFT v1 · #54214 · protein
HCV-H77 NS5B apo polymerase
2XI2 · RNA-directed RNA polymerase: “HCV-H77 NS5B apo polymerase”. X-ray diffraction, 1 ligand (SO4), 17 pockets (best druggability 0.80). MolNFT v1 #54214 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2XI2
- Type
- protein
- Length
- 1,682 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase
- EC
- 2.7.7.48
- UniProt
- P27958
- Ligands
- SO4
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 562 | 49% helix, 15% strand | P27958 |
| B | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 559 | 49% helix, 15% strand | P27958 |
| C | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 561 | 49% helix, 15% strand | P27958 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 20 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.80 | 0.81 | 79 | SO4 |
| 2 | 1039 | 0.80 | 0.81 | 82 | SO4 |
| 3 | 1066 | 0.80 | 0.81 | 83 | SO4 |
| 4 | 774 | 0.75 | 0.79 | 85 | empty |
| 5 | 885 | 0.74 | 0.78 | 74 | empty |
Interfaces
2 interfaces between chains.
- A–C · 470 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 323 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2XI2 · HCV-H77 NS5B Apo Polymerase · 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 P27958
- Elsewhere: RCSB PDB 2XI2 · PDBe 2XI2 · UniProt P27958
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