MolNFT v1 · #61009 · protein

RNase a- 5'-deoxy-5'-N-piperidinothymidine complex

3D8Y · Ribonuclease pancreatic: “RNase a- 5'-deoxy-5'-N-piperidinothymidine complex”. X-ray diffraction, 1 ligand (T3S), 3 pockets (best druggability 0.44). MolNFT v1 #61009 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3D8Y
Type: protein
Length: 248 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonuclease pancreatic
EC: 3.1.27.5
UniProt: P61823
Ligands: T3S
Pockets: 3 · best druggability 0.44

Structure

x-ray diffraction · 1 distinct chain · 21% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ribonuclease pancreatic (EC 3.1.27.5)	protein	124	21% helix, 35% strand	P61823

Ligands and binding sites

T3S · 5'-deoxy-5'-piperidin-1-ylthymidine · ligand · chains A
FLC · Citrate anion · additive · 2 copies · chains A

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	142	0.44	0.76	28	empty
2	59	0.34	0.78	13	empty
3	51	0.24	0.73	20	T3S

Interfaces

1 interface between chains.

A–B · 324 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

3D8Y · RNase A- 5'-Deoxy-5'-N-piperidinothymidine complex · the same entry in another collection · chain A against A, TM-score 1.00

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 P61823
Elsewhere: RCSB PDB 3D8Y · PDBe 3D8Y · UniProt P61823

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