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Ribonuclease T1 in complex with 2'GMP (form II crystal)

Analyse Ribonuclease T1 in complex with 2'GMP (form II crystal) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1I0X
Type: protein
Length: 415 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Guanyl-specific ribonuclease T1
EC: 3.1.27.3
UniProt: P00651
Ligands: 2GP, CA
Pockets: 2 · best druggability 0.45

Structure

x-ray diffraction · 2 distinct chains · 15% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Guanyl-specific ribonuclease T1 (EC 3.1.27.3)	protein	104	15% helix, 29% strand	P00651
D	Guanyl-specific ribonuclease T1 (EC 3.1.27.3)	protein	103	16% helix, 31% strand	P00651

Ligands and binding sites

2GP · Guanosine-2'-monophosphate · ligand · 5 copies · chains A, B, C, D
CA · Calcium ion · metal · 5 copies · chains B, C, 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	218	0.45	0.73	32	empty
2	110	0.37	0.75	31	empty

Interfaces

3 interfaces between chains.

A–C · 485 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 154 Å² buried · 1 hydrogen bond · protein-protein
A–D · 37 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

1I0X · Ribonuclease T1 in complex with 2'GMP (form II crystal) · 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 D 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 1I0X · PDBe 1I0X · UniProt P00651

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