MolNFT v1 · #26546 · protein
Co-crystal structure of E.COLI RNase hi active site mutant (E48A/D134N*) with MN2+
1WSG · Ribonuclease hi: “Co-crystal structure of E.COLI RNase hi active site mutant (E48A/D134N*) with MN2+”. X-ray diffraction, 1 ligand (MN), 5 pockets (best druggability 0.59). MolNFT v1 #26546 on GenesisL1: 3D structure, binding sites…
- PDB
- 1WSG
- Type
- protein
- Length
- 616 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease hi
- EC
- 3.1.26.4
- UniProt
- P0A7Y4
- Ligands
- MN
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Ribonuclease hi (EC 3.1.26.4) | protein | 155 | 35% helix, 31% strand | P0A7Y4 |
| C | Ribonuclease hi (EC 3.1.26.4) | protein | 151 | 36% helix, 28% strand | P0A7Y4 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 305 | 0.59 | 0.78 | 33 | empty |
| 2 | 244 | 0.56 | 0.78 | 27 | empty |
| 3 | 56 | 0.34 | 0.78 | 13 | empty |
| 4 | 62 | 0.26 | 0.72 | 11 | empty |
| 5 | 57 | 0.26 | 0.72 | 12 | empty |
Interfaces
2 interfaces between chains.
- B–D · 735 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 338 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1WSG · Co-crystal structure of E.coli RNase HI active site mutant (E48A/D134N*) with Mn2+ · the same entry in another collection · chain A against A, TM-score 1.00
- P0A7Y4 · AlphaFold monomer V2.0 prediction for ribonuclease hi (P0A7Y4) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P0A7Y4
- Elsewhere: RCSB PDB 1WSG · PDBe 1WSG · UniProt P0A7Y4
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