MolNFT v1 · #136993 · protein + DNA + RNA
Bhrnase H - amide-RNA/DNA complex
5VAJ · RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*(URU)P*C)-3'): “Bhrnase H - amide-RNA/DNA complex”. X-ray diffraction, 1 ligand (MG). MolNFT v1 #136993 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VAJ
- Type
- protein + DNA + RNA
- Length
- 294 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*(URU)P*C)-3'); DNA…
- EC
- 3.1.26.4
- UniProt
- Q9KEI9
- Ligands
- MG
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*(URU)P*C)-3') | rna | 11 | — | — |
| D | DNA (5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3') | dna | 12 | — | — |
| A | Ribonuclease H (EC 3.1.26.4) | protein | 135 | 36% helix, 24% strand | Q9KEI9 |
| B | Ribonuclease H (EC 3.1.26.4) | protein | 136 | 34% helix, 26% strand | Q9KEI9 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains C, A, B
- GOL · Glycerol · additive · 9 copies · chains C, D, A, B
- ACT · Acetate ion · additive · 3 copies · chains D, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
5 interfaces between chains.
- C–D · 583 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- C–A · 482 Ų buried · 23 hydrogen bonds · protein-nucleic
- C–B · 478 Ų buried · 22 hydrogen bonds · protein-nucleic
- D–B · 418 Ų buried · 14 hydrogen bonds · protein-nucleic
- D–A · 413 Ų buried · 14 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
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 5VAJ · PDBe 5VAJ · UniProt Q9KEI9
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