Research workbench
Bacillus halodurans RNase H catalytic domain mutant D132N in complex with 12-mer RNA/DNA hybrid
Analyse Bacillus halodurans RNase H catalytic domain mutant D132N in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZBI
- Type
- protein + DNA + RNA
- Length
- 295 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*C)-3'; 5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3'…
- EC
- 3.1.26.4
- UniProt
- Q9KEI9
- Ligands
- MG
- Pockets
- 2 · best druggability 0.39
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*C)-3' | rna | 12 | — | — |
| D | 5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3' | dna | 12 | — | — |
| A | Ribonuclease H-related protein (EC 3.1.26.4) | protein | 135 | 36% helix, 24% strand | Q9KEI9 |
| B | Ribonuclease H-related protein (EC 3.1.26.4) | protein | 136 | 33% helix, 26% strand | Q9KEI9 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains C, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.39 | 0.78 | 10 | empty |
| 2 | 58 | 0.33 | 0.76 | 10 | empty |
Interfaces
5 interfaces between chains.
- C–D · 584 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- C–A · 521 Ų buried · 23 hydrogen bonds · protein-nucleic
- C–B · 448 Ų buried · 19 hydrogen bonds · protein-nucleic
- D–A · 420 Ų buried · 15 hydrogen bonds · protein-nucleic
- D–B · 391 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 1ZBI · Bacillus halodurans RNase H catalytic domain mutant D132N in complex with 12-mer RNA/DNA… · the same entry in another collection · chain C against C, TM-score 1.00
- Q9KEI9 · AlphaFold monomer V2.0 prediction for ribonuclease H (Q9KEI9) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 1ZBI · PDBe 1ZBI · UniProt Q9KEI9
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