MolNFT v1 · #3093 · protein

RNase T1 variant with altered guanine binding segment

1CH0 · Protein (ribonuclease T1): “RNase T1 variant with altered guanine binding segment”. X-ray diffraction, 3 ligands (2GP, CA, CL), 5 pockets (best druggability 0.53). MolNFT v1 #3093 on GenesisL1: 3D structure, binding sites and…

PDB: 1CH0
Type: protein
Length: 312 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (ribonuclease T1)
EC: 3.1.27.3
UniProt: P00651
Ligands: 2GP, CA, CL
Pockets: 5 · best druggability 0.53

Structure

x-ray diffraction · 1 distinct chain · 16% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Protein (ribonuclease T1) (EC 3.1.27.3)	protein	104	16% helix, 29% strand	P00651

Ligands and binding sites

2GP · Guanosine-2'-monophosphate · ligand · 2 copies · chains A, B, C
CA · Calcium ion · metal · 4 copies · chains A, B, C
CL · Chloride ion · ion · chains C

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

Pockets

5 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	194	0.53	0.78	38	empty
2	121	0.48	0.79	24	CA, 2GP
3	145	0.43	0.76	30	empty
4	57	0.39	0.80	12	2GP
5	90	0.37	0.76	19	CA

Interfaces

2 interfaces between chains.

A–B · 454 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 413 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

1CH0 · RNase T1 variant with altered guanine binding segment · the same entry in another collection · chain A against A, TM-score 1.00
P00651 · AlphaFold monomer V2.0 prediction for guanyl-specific ribonuclease T1 (P00651) · a predicted model of the same protein · chain A 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 P00651
Elsewhere: RCSB PDB 1CH0 · PDBe 1CH0 · UniProt P00651

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