Research workbench

Crystal structure of RSA4 in complex with the NSA2 binding peptide

Analyse Crystal structure of RSA4 in complex with the NSA2 binding peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4WJV
Type: protein
Length: 3,032 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribosome assembly protein 4; Maltose-binding periplasmic protein; Ribosome biogenesis…
UniProt: P25382, P0AEX9, P40078
Ligands: GLC, SO4
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 5 distinct chains · 32% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Ribosome assembly protein 4	protein	378	7% helix, 46% strand	P25382
E, G, H	Maltose-binding periplasmic protein	protein	369	45% helix, 20% strand	P0AEX9
F	Maltose-binding periplasmic protein	protein	368	45% helix, 20% strand	P0AEX9
I, J, L	Ribosome biogenesis protein NSA2	protein	11	0% helix, 0% strand	P40078
K	Ribosome biogenesis protein NSA2	protein	12	0% helix, 0% strand	P40078

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 8 copies · chains E, F, G, H
SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	671	0.88	0.92	65	empty
2	653	0.88	0.92	70	empty
3	640	0.88	0.92	64	empty
4	600	0.87	0.93	64	empty
5	339	0.76	0.87	33	GLC

Interfaces

16 interfaces between chains.

C–I · 688 Å² buried · 7 hydrogen bonds · protein-protein
B–L · 683 Å² buried · 4 hydrogen bonds · protein-protein
A–K · 666 Å² buried · 4 hydrogen bonds · protein-protein
D–J · 665 Å² buried · 4 hydrogen bonds · protein-protein
C–E · 373 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4WJV · Crystal structure of Rsa4 in complex with the Nsa2 binding peptide · the same entry in another collection · chain L against L, 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 P25382
Every structure of UniProt P0AEX9
Every structure of UniProt P40078
Elsewhere: RCSB PDB 4WJV · PDBe 4WJV · UniProt P25382 · UniProt P0AEX9 · UniProt P40078

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