MolNFT v1 · #160839 · protein

RNase a in complex with P5U

6PVX · Ribonuclease pancreatic: “RNase a in complex with P5U”. X-ray diffraction, 1 ligand (U5F), 2 pockets (best druggability 0.39). MolNFT v1 #160839 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6PVX
Type: protein
Length: 248 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonuclease pancreatic
EC: 4.6.1.18
UniProt: P61823
Ligands: U5F
Pockets: 2 · best druggability 0.39

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ribonuclease pancreatic (EC 4.6.1.18)	protein	124	21% helix, 35% strand	P61823

Ligands and binding sites

U5F · 5'-O-[(R)-hydroxy{[(s)-hydroxy{[(s)-hydroxy{[(s)-hydroxy(phosphonooxy) phosphoryl]oxy}phosphoryl]oxy}phosphoryl]oxy}phosphory l]uridine · ligand · 3 copies · chains A, B

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	80	0.39	0.78	15	empty
2	112	0.39	0.75	20	empty

Interfaces

1 interface between chains.

A–B · 324 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

6PVX · RNase A in complex with p5U · 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 6PVX · PDBe 6PVX · UniProt P61823

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