MolNFT v1 · #97347 · protein + DNA
Crystal structure of RNase T in complex with a bluge DNA (two nucleotide insertion ct )
4KB1 · Ribonuclease T: “Crystal structure of RNase T in complex with a bluge DNA (two nucleotide insertion ct )”. X-ray diffraction, 1 ligand (MG), 2 pockets (best druggability 0.75). MolNFT v1 #97347 on GenesisL1: 3D structure, binding…
- PDB
- 4KB1
- Type
- protein + DNA
- Length
- 449 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease T; Bulge DNA
- EC
- 3.1.13.-
- UniProt
- P30014
- Ligands
- MG
- Pockets
- 2 · best druggability 0.75
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 | 208 | 41% helix, 24% strand | P30014 |
| B | Ribonuclease T (EC 3.1.13.-) | protein | 205 | 39% helix, 24% strand | P30014 |
| C, D | Bulge DNA | 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
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1121 | 0.75 | 0.78 | 95 | empty |
| 2 | 82 | 0.41 | 0.79 | 16 | MG |
Interfaces
5 interfaces between chains.
- A–B · 1367 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 609 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–D · 607 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–D · 325 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–C · 314 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 4KB1 · Crystal structure of RNase T in complex with a bluge DNA (two nucleotide insertion CT ) · 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 4KB1 · PDBe 4KB1 · UniProt P30014
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