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MolNFT v1 · #121211 · protein

Ribonuclease T1 (ASN9ALA/THR93ALA doublemutant) complexed with 2'GMP

5HOH · Protein (ribonuclease T1): “Ribonuclease T1 (ASN9ALA/THR93ALA doublemutant) complexed with 2'GMP”. X-ray diffraction, 2 ligands (2GP, CA), 3 pockets (best druggability 0.43). MolNFT v1 #121211 on GenesisL1: 3D structure, binding…

PDB
5HOH
Type
protein
Length
416 residues
Chains
4
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
Pockets
3 · best druggability 0.43

Structure

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

ChainMoleculeTypeResiduesSecondary structureUniProt
A, B, C, DProtein (ribonuclease T1) (EC 3.1.27.3)protein10416% helix, 29% strandP00651

Ligands and binding sites

  • 2GP · Guanosine-2'-monophosphate · ligand · 5 copies · chains A, B, C, D
  • CA · Calcium ion · metal · 2 copies · chains D

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11750.430.7321empty
21300.410.7533empty
3560.300.76172GP

Interfaces

3 interfaces between chains.

  • A–C · 468 Ų buried · 10 hydrogen bonds · protein-protein
  • B–C · 181 Ų buried · 0 hydrogen bonds · protein-protein
  • A–D · 17 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

  • 5HOH · Ribonuclease T1 (ASN9ALA/THR93ALA doublemutant) complexed with 2'GMP · the same entry in another collection · chain A against A, TM-score 1.00

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