MolNFT v1 · #12475 · protein
Crystal structure of rabbit hemorrhagic disease virus RNA-dependent RNA polymerase complexed with MN2+
1KHW · RNA-directed RNA polymerase: “Crystal structure of rabbit hemorrhagic disease virus RNA-dependent RNA polymerase complexed with MN2+”. X-ray diffraction, 1 ligand (MN), 10 pockets (best druggability 0.71). MolNFT v1 #12475 on…
- PDB
- 1KHW
- Type
- protein
- Length
- 990 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase
- EC
- 2.7.7.48
- UniProt
- P27410
- Ligands
- MN
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 493 | 42% helix, 18% strand | P27410 |
| B | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 497 | 42% helix, 18% strand | P27410 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.71 | 0.75 | 111 | MN |
| 2 | 517 | 0.65 | 0.77 | 55 | empty |
| 3 | 339 | 0.59 | 0.77 | 43 | empty |
| 4 | 415 | 0.56 | 0.74 | 41 | MN |
| 5 | 90 | 0.47 | 0.81 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 698 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1KHW · Crystal Structure of Rabbit Hemorrhagic Disease Virus RNA-dependent RNA 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 P27410
- Elsewhere: RCSB PDB 1KHW · PDBe 1KHW · UniProt P27410
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