MolNFT v1 · #72722 · protein + DNA

Crystal structure of RNase T in complex with a non-preferred ssdna (aac)

3NH0 · Ribonuclease T: “Crystal structure of RNase T in complex with a non-preferred ssdna (aac)”. X-ray diffraction, 3 pockets (best druggability 0.62). MolNFT v1 #72722 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3NH0
Type: protein + DNA
Length: 420 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonuclease T; 5'-D(*TP*TP*AP*CP*AP*AP*C)-3'
EC: 3.1.13.-
UniProt: P30014
Pockets: 3 · best druggability 0.62

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	206	42% helix, 24% strand	P30014
B	Ribonuclease T (EC 3.1.13.-)	protein	208	42% helix, 24% strand	P30014
C, D	5'-D(TPTPAPCPAPAP*C)-3'	dna	3	—	—

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	420	0.62	0.77	38	empty
2	69	0.42	0.81	16	empty
3	71	0.33	0.76	12	empty

Interfaces

5 interfaces between chains.

A–B · 1427 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 504 Å² buried · 10 hydrogen bonds · protein-nucleic
A–C · 490 Å² buried · 12 hydrogen bonds · protein-nucleic
A–D · 162 Å² buried · 2 hydrogen bonds · protein-nucleic
B–C · 159 Å² buried · 1 hydrogen bond · protein-nucleic

Compared structures

3NH0 · Crystal structure of RNase T in complex with a non-preferred ssDNA (AAC) · 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 A 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 3NH0 · PDBe 3NH0 · UniProt P30014

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