Research workbench
The structure of the human RNase H2 complex defines key interaction interfaces relevant to enzyme function and human disease
Analyse The structure of the human RNase H2 complex defines key interaction interfaces… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P56
- Type
- protein
- Length
- 1,020 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease H2 subunit a; Ribonuclease H2 subunit B; Ribonuclease H2 subunit C
- EC
- 3.1.26.4
- UniProt
- O75792, Q5TBB1, Q8TDP1
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease H2 subunit a (EC 3.1.26.4) | protein | 249 | 44% helix, 18% strand | O75792 |
| B | Ribonuclease H2 subunit B | protein | 156 | 35% helix, 23% strand | Q5TBB1 |
| C, F | Ribonuclease H2 subunit C | protein | 116 | 19% helix, 40% strand | Q8TDP1 |
| D | Ribonuclease H2 subunit a (EC 3.1.26.4) | protein | 225 | 44% helix, 17% strand | O75792 |
| E | Ribonuclease H2 subunit B | protein | 158 | 34% helix, 25% strand | Q5TBB1 |
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.72 | 0.88 | 32 | empty |
| 2 | 551 | 0.71 | 0.79 | 76 | empty |
| 3 | 522 | 0.69 | 0.79 | 73 | empty |
| 4 | 169 | 0.69 | 0.88 | 29 | empty |
| 5 | 154 | 0.63 | 0.85 | 32 | empty |
Interfaces
6 interfaces between chains.
- E–F · 2388 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 2355 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 1388 Ų buried · 24 hydrogen bonds · protein-protein
- D–F · 1344 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 815 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3P56 · The structure of the human RNase H2 complex defines key interaction interfaces relevant… · the same entry in another collection · chain F against F, TM-score 1.00
- O75792 · AlphaFold monomer V2.0 prediction for ribonuclease H2 subunit a (O75792) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q8TDP1 · AlphaFold monomer V2.0 prediction for ribonuclease H2 subunit C (Q8TDP1) · a predicted model of the same protein · chain C against A, TM-score 0.97
- Q5TBB1 · AlphaFold monomer V2.0 prediction for ribonuclease H2 subunit B (Q5TBB1) · a predicted model of the same protein · chain E against A, TM-score 0.96
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 O75792
- Every structure of UniProt Q5TBB1
- Every structure of UniProt Q8TDP1
- Elsewhere: RCSB PDB 3P56 · PDBe 3P56 · UniProt O75792 · UniProt Q5TBB1 · UniProt Q8TDP1
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