MolNFT v1 · #72724 · protein + DNA
Crystal structure of RNase T in complex with a stem DNA with a 3' overhang
3NH2 · Ribonuclease T: “Crystal structure of RNase T in complex with a stem DNA with a 3' overhang”. X-ray diffraction, 8 pockets (best druggability 0.84). MolNFT v1 #72724 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3NH2
- Type
- protein + DNA
- Length
- 842 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease T; 5'-D(P*TP*TP*AP*CP*AP*AP*C)-3'
- EC
- 3.1.13.-
- UniProt
- P30014
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Ribonuclease T (EC 3.1.13.-) | protein | 202 | 42% helix, 24% strand | P30014 |
| B, E | Ribonuclease T (EC 3.1.13.-) | protein | 206 | 41% helix, 24% strand | P30014 |
| C, H | 5'-D(P*TP*TP*AP*CP*AP*AP*C)-3' | dna | 7 | — | — |
| D, G | 5'-D(P*TP*TP*AP*CP*AP*AP*C)-3' | dna | 6 | — | — |
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 931 | 0.84 | 0.85 | 112 | empty |
| 2 | 620 | 0.70 | 0.78 | 47 | empty |
| 3 | 364 | 0.65 | 0.80 | 37 | empty |
| 4 | 206 | 0.52 | 0.77 | 31 | empty |
| 5 | 152 | 0.52 | 0.80 | 29 | empty |
Interfaces
17 interfaces between chains.
- E–F · 1400 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1394 Ų buried · 14 hydrogen bonds · protein-protein
- F–H · 468 Ų buried · 13 hydrogen bonds · protein-nucleic
- E–G · 467 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–C · 463 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3NH2 · Crystal structure of RNase T in complex with a stem DNA with a 3' overhang · the same entry in another collection · chain H against H, TM-score 1.00
- P30014 · AlphaFold monomer V2.0 prediction for ribonuclease T (P30014) · 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 P30014
- Elsewhere: RCSB PDB 3NH2 · PDBe 3NH2 · UniProt P30014
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