MolNFT v1 · #74723 · protein
The structure of the human RNase H2 complex defines key interaction interfaces relevant to enzyme function and human disease
3P56 · Ribonuclease H2 subunit a: “The structure of the human RNase H2 complex defines key interaction interfaces relevant to enzyme function…”. X-ray diffraction, 20 pockets (best druggability 0.72). MolNFT v1 #74723 on GenesisL1: 3D…
- 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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