MolNFT v1 · #72721 · protein + DNA
Crystal structure of RNase T in complex with a non-preferred ssdna (gc) with one mg in the active site
3NGZ · Ribonuclease T: “Crystal structure of RNase T in complex with a non-preferred ssdna (gc) with one mg in the active site”. X-ray diffraction, 2 ligands (MG, CO), 3 pockets (best druggability 0.66). MolNFT v1 #72721 on GenesisL1: 3D…
- PDB
- 3NGZ
- Type
- protein + DNA
- Length
- 417 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease T; 5'-D(P*GP*C)-3'
- EC
- 3.1.13.-
- UniProt
- P30014
- Ligands
- MG, CO
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease T (EC 3.1.13.-) | protein | 207 | 42% helix, 24% strand | P30014 |
| B | Ribonuclease T (EC 3.1.13.-) | protein | 206 | 43% helix, 24% strand | P30014 |
| C, D | 5'-D(P*GP*C)-3' | dna | 2 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, C, B, D
- CO · Cobalt (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 458 | 0.66 | 0.78 | 41 | empty |
| 2 | 85 | 0.48 | 0.82 | 18 | MG |
| 3 | 60 | 0.47 | 0.84 | 17 | MG |
Interfaces
5 interfaces between chains.
- A–B · 1379 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 380 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–D · 375 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–D · 87 Ų buried · 0 hydrogen bonds · protein-nucleic
- B–C · 84 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 3NGZ · Crystal structure of RNase T in complex with a non-preferred ssDNA (GC) with one Mg in… · the same entry in another collection · chain A against A, TM-score 1.00
- P30014 · AlphaFold monomer V2.0 prediction for ribonuclease T (P30014) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 3NGZ · PDBe 3NGZ · UniProt P30014
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