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Crystal structure of escherichia COLI RNase T

Analyse Crystal structure of escherichia COLI RNase T in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2IS3
Type: protein
Length: 781 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonuclease T
EC: 3.1.13.-
UniProt: P30014
Ligands: SO4
Pockets: 8 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	Ribonuclease T (EC 3.1.13.-)	protein	203	40% helix, 23% strand	P30014
B	Ribonuclease T (EC 3.1.13.-)	protein	172	46% helix, 27% strand	P30014

Ligands and binding sites

SO4 · Sulfate ion · ion · 13 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1146	0.78	0.80	87	SO4
2	76	0.73	0.97	27	empty
3	652	0.69	0.77	67	SO4
4	60	0.57	0.90	18	empty
5	236	0.51	0.76	35	empty

Interfaces

4 interfaces between chains.

A–B · 1407 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 1370 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 601 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 480 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 modified (engineered).

Compared structures

2IS3 · Crystal Structure of Escherichia coli RNase T · 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 2IS3 · PDBe 2IS3 · UniProt P30014

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