MolNFT v1 · #97346 · protein + DNA
Crystal structure of RNase T in complex with a bluge DNA (two nucleotide insertion cc )
4KB0 · Ribonuclease T: “Crystal structure of RNase T in complex with a bluge DNA (two nucleotide insertion cc )”. X-ray diffraction, 1 ligand (MG), 3 pockets (best druggability 0.76). MolNFT v1 #97346 on GenesisL1: 3D structure, binding…
- PDB
- 4KB0
- Type
- protein + DNA
- Length
- 447 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease T; DNA (5'- D(*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*CP*C)-3')
- EC
- 3.1.13.-
- UniProt
- P30014
- Ligands
- MG
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease T (EC 3.1.13.-) | protein | 207 | 41% helix, 24% strand | P30014 |
| B | Ribonuclease T (EC 3.1.13.-) | protein | 204 | 39% helix, 25% strand | P30014 |
| C, D | DNA (5'- D(*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*CP*C)-3') | dna | 18 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, C, B, D
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 | 955 | 0.76 | 0.79 | 84 | empty |
| 2 | 190 | 0.50 | 0.77 | 21 | empty |
| 3 | 136 | 0.42 | 0.76 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1382 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 600 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–C · 600 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–C · 343 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–D · 339 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 4KB0 · Crystal structure of RNase T in complex with a bluge DNA (Two nucleotide insertion CC ) · 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 0.99
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 4KB0 · PDBe 4KB0 · UniProt P30014
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.