MolNFT v1 · #146691 · protein + DNA + RNA
Crystal structure of bacillus halodurans ribonuclease H1 in complex with an RNA/DNA hybrid: reaction in 20 mm MG2+ and 75 mm K+ for 40 S at 21 C
6DP4: “Crystal structure of bacillus halodurans ribonuclease H1 in complex with an RNA/DNA hybrid: reaction in 20 mm…”. X-ray diffraction, 3 ligands (K, MG, IOD), 1 pocket (best druggability 0.34). MolNFT v1 #146691 on GenesisL1: 3D…
- PDB
- 6DP4
- Type
- protein + DNA + RNA
- Length
- 148 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease H; 5'-R(*AP*CP*AP*U)-3' portion of cleaved RNA 5'- R(*AP*CP*AP*UP*CP*G)-3'…
- EC
- 3.1.26.4
- UniProt
- Q9KEI9
- Ligands
- K, MG, IOD
- Pockets
- 1 · best druggability 0.34
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease H (EC 3.1.26.4) | protein | 136 | 33% helix, 26% strand | Q9KEI9 |
| B | 5'-R(*AP*CP*AP*U)-3' portion of cleaved RNA 5'- R(*AP*CP*AP*UP*CP*G)-3' | rna | 4 | — | — |
| b | 5'-R(P*CP*G)-3' portion of cleaved RNA 5'- R(*AP*CP*AP*UP*CP*G)-3' | rna | 2 | — | — |
| C | DNA (5'-D(*CP*GP*AP*TP*GP*T)-3') | dna | 6 | — | — |
Ligands and binding sites
- K · Potassium ion · metal · 3 copies · chains A, b, B, C
- MG · Magnesium ion · metal · 2 copies · chains A, b, B
- IOD · Iodide ion · ion · 3 copies · chains A
- GOL · Glycerol · additive · 7 copies · chains A, b, C
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 | 51 | 0.34 | 0.78 | 11 | IOD |
Interfaces
6 interfaces between chains.
- A–C · 438 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–b · 319 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–B · 266 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–C · 189 Ų buried · 12 hydrogen bonds · nucleic-nucleic
- b–C · 145 Ų buried · 10 hydrogen bonds · nucleic-nucleic
Compared structures
- 6DP4 · Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with an RNA/DNA… · 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 Q9KEI9
- Elsewhere: RCSB PDB 6DP4 · PDBe 6DP4 · UniProt Q9KEI9
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