Research workbench

Crystal structure of nprr in complex with its cognate peptide nprx

Analyse Crystal structure of nprr in complex with its cognate peptide nprx in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4GPK
Type: protein
Length: 4,208 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nprr; Nprx peptide
UniProt: G5DDY8
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 13 distinct chains · 77% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nprr	protein	343	79% helix, 0% strand	G5DDY8
B	Nprr	protein	342	72% helix, 0% strand	G5DDY8
C	Nprr	protein	340	75% helix, 0% strand	G5DDY8
D	Nprr	protein	342	79% helix, 0% strand	G5DDY8
E	Nprr	protein	339	75% helix, 0% strand	G5DDY8
F	Nprr	protein	341	78% helix, 0% strand	G5DDY8
G	Nprr	protein	345	78% helix, 0% strand	G5DDY8
H	Nprr	protein	343	79% helix, 0% strand	G5DDY8
I	Nprr	protein	344	77% helix, 0% strand	G5DDY8
J	Nprr	protein	347	79% helix, 0% strand	G5DDY8
K	Nprr	protein	340	75% helix, 0% strand	G5DDY8
L	Nprr	protein	346	77% helix, 0% strand	G5DDY8
M, N, O, P, Q, R, S, T, U, V, W, X	Nprx peptide	protein	8	0% helix, 0% strand	—

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	757	0.80	0.84	84	empty
2	1056	0.80	0.81	92	empty
3	689	0.79	0.84	81	empty
4	374	0.77	0.87	50	empty
5	757	0.77	0.81	52	empty

Interfaces

30 interfaces between chains.

A–B · 1142 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 1033 Å² buried · 14 hydrogen bonds · protein-protein
I–J · 1031 Å² buried · 6 hydrogen bonds · protein-protein
I–L · 1031 Å² buried · 5 hydrogen bonds · protein-protein
G–H · 1022 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4GPK · Crystal structure of NprR in complex with its cognate peptide NprX · the same entry in another collection · chain G against G, 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 G5DDY8
Elsewhere: RCSB PDB 4GPK · PDBe 4GPK · UniProt G5DDY8

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.