MolNFT v1 · #72723 · protein + DNA
Crystal structure of RNase T in complex with a preferred ssdna (tagg) with two mg in the active site
3NH1 · Ribonuclease T: “Crystal structure of RNase T in complex with a preferred ssdna (tagg) with two mg in the active site”. X-ray diffraction, 1 ligand (MG), 7 pockets (best druggability 0.62). MolNFT v1 #72723 on GenesisL1: 3D…
- PDB
- 3NH1
- 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(*TP*TP*AP*TP*AP*GP*G)-3'
- EC
- 3.1.13.-
- UniProt
- P30014
- Ligands
- MG
- Pockets
- 7 · best druggability 0.62
Structure
x-ray diffraction · 6 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribonuclease T (EC 3.1.13.-) | protein | 209 | 41% helix, 23% strand | P30014 |
| C | Ribonuclease T (EC 3.1.13.-) | protein | 204 | 40% helix, 24% strand | P30014 |
| D | Ribonuclease T (EC 3.1.13.-) | protein | 205 | 40% helix, 24% strand | P30014 |
| E | 5'-D(*TP*TP*AP*TP*AP*GP*G)-3' | dna | 4 | — | — |
| F | 5'-D(*TP*TP*AP*TP*AP*GP*G)-3' | dna | 5 | — | — |
| G, H | 5'-D(*TP*TP*AP*TP*AP*GP*G)-3' | dna | 3 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, E, B, F, C, G, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 390 | 0.62 | 0.77 | 38 | empty |
| 2 | 411 | 0.60 | 0.76 | 34 | empty |
| 3 | 361 | 0.59 | 0.76 | 42 | empty |
| 4 | 98 | 0.55 | 0.85 | 21 | empty |
| 5 | 76 | 0.48 | 0.83 | 21 | MG |
Interfaces
11 interfaces between chains.
- C–D · 1385 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1320 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 654 Ų buried · 12 hydrogen bonds · protein-protein
- C–G · 579 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–F · 554 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 3NH1 · Crystal structure of RNase T in complex with a preferred ssDNA (TAGG) with two Mg in the… · 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 C against A, TM-score 0.99
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 3NH1 · PDBe 3NH1 · UniProt P30014
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