Research workbench
Crystal structure of human RNase H2 complex
Analyse Crystal structure of human RNase H2 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PUF
- Type
- protein
- Length
- 3,465 residues
- Chains
- 18
- 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 0.79
Structure
x-ray diffraction · 18 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease H2 subunit a (EC 3.1.26.4) | protein | 270 | 41% helix, 19% strand | O75792 |
| B | Ribonuclease H2 subunit B (EC 3.1.26.4) | protein | 185 | 40% helix, 28% strand | Q5TBB1 |
| C | Ribonuclease H2 subunit C (EC 3.1.26.4) | protein | 127 | 22% helix, 40% strand | Q8TDP1 |
| D | Ribonuclease H2 subunit a (EC 3.1.26.4) | protein | 274 | 38% helix, 19% strand | O75792 |
| E | Ribonuclease H2 subunit B (EC 3.1.26.4) | protein | 181 | 38% helix, 25% strand | Q5TBB1 |
| F | Ribonuclease H2 subunit C (EC 3.1.26.4) | protein | 128 | 18% helix, 43% strand | Q8TDP1 |
| G | Ribonuclease H2 subunit a (EC 3.1.26.4) | protein | 266 | 40% helix, 19% strand | O75792 |
| H | Ribonuclease H2 subunit B (EC 3.1.26.4) | protein | 202 | 35% helix, 25% strand | Q5TBB1 |
| I | Ribonuclease H2 subunit C (EC 3.1.26.4) | protein | 140 | 17% helix, 39% strand | Q8TDP1 |
| J | Ribonuclease H2 subunit a (EC 3.1.26.4) | protein | 270 | 40% helix, 19% strand | O75792 |
| K | Ribonuclease H2 subunit B (EC 3.1.26.4) | protein | 182 | 38% helix, 28% strand | Q5TBB1 |
| L | Ribonuclease H2 subunit C (EC 3.1.26.4) | protein | 116 | 14% helix, 41% strand | Q8TDP1 |
| M | Ribonuclease H2 subunit a (EC 3.1.26.4) | protein | 272 | 41% helix, 20% strand | O75792 |
| N | Ribonuclease H2 subunit B (EC 3.1.26.4) | protein | 186 | 34% helix, 26% strand | Q5TBB1 |
| O | Ribonuclease H2 subunit C (EC 3.1.26.4) | protein | 116 | 14% helix, 43% strand | Q8TDP1 |
| P | Ribonuclease H2 subunit a (EC 3.1.26.4) | protein | 259 | 41% helix, 19% strand | O75792 |
| Q | Ribonuclease H2 subunit B (EC 3.1.26.4) | protein | 176 | 36% helix, 26% strand | Q5TBB1 |
| R | Ribonuclease H2 subunit C (EC 3.1.26.4) | protein | 115 | 15% helix, 42% strand | Q8TDP1 |
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1147 | 0.79 | 0.81 | 126 | empty |
| 2 | 1102 | 0.76 | 0.79 | 133 | empty |
| 3 | 1066 | 0.75 | 0.78 | 119 | empty |
| 4 | 374 | 0.59 | 0.76 | 45 | empty |
| 5 | 151 | 0.56 | 0.81 | 24 | empty |
Interfaces
53 interfaces between chains.
- H–I · 3191 Ų buried · 55 hydrogen bonds · protein-protein
- E–F · 2820 Ų buried · 55 hydrogen bonds · protein-protein
- B–C · 2772 Ų buried · 50 hydrogen bonds · protein-protein
- N–O · 2602 Ų buried · 42 hydrogen bonds · protein-protein
- K–L · 2520 Ų buried · 48 hydrogen bonds · protein-protein
Compared structures
- 3PUF · Crystal structure of human RNase H2 complex · the same entry in another collection · chain H against H, 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 O75792
- Every structure of UniProt Q5TBB1
- Every structure of UniProt Q8TDP1
- Elsewhere: RCSB PDB 3PUF · PDBe 3PUF · UniProt O75792 · UniProt Q5TBB1 · UniProt Q8TDP1
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