MolNFT v1 · #134186 · protein + DNA
Bacillus halodurans RNase H mutant D132N in complex with 12-mer FRNA/DNA hybrid
5SWM · Ribonuclease H: “Bacillus halodurans RNase H mutant D132N in complex with 12-mer FRNA/DNA hybrid”. X-ray diffraction, 2 ligands (NA, CL), 1 pocket (best druggability 0.34). MolNFT v1 #134186 on GenesisL1: 3D structure, binding sites…
- PDB
- 5SWM
- Type
- protein + DNA
- Length
- 288 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease H; RNA (12-mer); DNA (12-mer)
- EC
- 3.1.26.4
- UniProt
- Q9KEI9
- Ligands
- NA, CL
- Pockets
- 1 · best druggability 0.34
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease H (EC 3.1.26.4) | protein | 131 | 34% helix, 24% strand | Q9KEI9 |
| B | Ribonuclease H (EC 3.1.26.4) | protein | 133 | 34% helix, 24% strand | Q9KEI9 |
| C | RNA (12-mer) | dna | 12 | — | — |
| D | DNA (12-mer) | dna | 12 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
- GOL · Glycerol · additive · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.34 | 0.77 | 11 | PEG |
Interfaces
5 interfaces between chains.
- C–D · 557 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- A–C · 480 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–D · 448 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–D · 433 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–C · 343 Ų buried · 14 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 13 modified (nucleotide modification).
Compared structures
- 5SWM · Bacillus halodurans RNase H mutant D132N in complex with 12-mer FRNA/DNA hybrid · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KEI9 · AlphaFold monomer V2.0 prediction for ribonuclease H (Q9KEI9) · a predicted model of the same protein · 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 Q9KEI9
- Elsewhere: RCSB PDB 5SWM · PDBe 5SWM · UniProt Q9KEI9
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