MolNFT v1 · #93937 · protein + DNA
T. maritima RNase H2 G21S in complex with nucleic acid substrate and calcium ions
4HHT · Ribonuclease hii: “T. maritima RNase H2 G21S in complex with nucleic acid substrate and calcium ions”. X-ray diffraction, 1 ligand (CA), 2 pockets (best druggability 0.30). MolNFT v1 #93937 on GenesisL1: 3D structure, binding sites…
- PDB
- 4HHT
- Type
- protein + DNA
- Length
- 244 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease hii; DNA (5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3'); DNA/RNA…
- EC
- 3.1.26.4
- UniProt
- Q9X017
- Ligands
- CA
- Pockets
- 2 · best druggability 0.30
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease hii (EC 3.1.26.4) | protein | 220 | 51% helix, 15% strand | Q9X017 |
| C | DNA (5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3') | dna | 12 | — | — |
| D | DNA/RNA (5'-D(*GP*AP*CP*AP*C)-R(P*C)-D(P*TP*GP*AP*TP*TP*C)- 3') | dna | 12 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.30 | 0.76 | 17 | empty |
| 2 | 86 | 0.29 | 0.72 | 11 | CA |
Interfaces
3 interfaces between chains.
- C–D · 551 Ų buried · 45 hydrogen bonds · nucleic-nucleic
- A–D · 545 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–C · 397 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 4HHT · T. maritima RNase H2 G21S in complex with nucleic acid substrate and calcium ions · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X017 · AlphaFold monomer V2.0 prediction for ribonuclease hii (Q9X017) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9X017
- Elsewhere: RCSB PDB 4HHT · PDBe 4HHT · UniProt Q9X017
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