Research workbench

Crystal structure of 3'SL bound artb

Analyse Crystal structure of 3'SL bound artb in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5WHU
Type: protein
Length: 1,195 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Artb protein
UniProt: Q404H3
Ligands: SIA, GAL, GLC, CA, CL
Pockets: 7 · best druggability 0.71

Structure

x-ray diffraction · 5 distinct chains · 18% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Artb protein	protein	120	17% helix, 42% strand	Q404H3
B, E	Artb protein	protein	119	17% helix, 42% strand	Q404H3
C, D, F, G, I	Artb protein	protein	118	17% helix, 42% strand	Q404H3
H	Artb protein	protein	124	23% helix, 43% strand	Q404H3
J	Artb protein	protein	123	16% helix, 44% strand	Q404H3

Ligands and binding sites

SIA · N-acetyl-alpha-neuraminic acid · sugar · 10 copies · chains A, C, D, E, H, I, J
GAL · beta-D-galactopyranose · sugar · 9 copies · chains A, C, D, E, H, I, J
GLC · alpha-D-glucopyranose · sugar · 6 copies · chains C, D, E, H, I, J
CA · Calcium ion · metal · 7 copies · chains B, E, F, I, G, H, A, D, J
CL · Chloride ion · ion · 23 copies · chains A, C, D, B, F, E, G, H, I, J
PEG · Di(hydroxyethyl)ether · additive · 12 copies · chains A, H, B, E, D, F, I, G, J, C
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 6 copies · chains B, C, D, G, H, J
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains E, H

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

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	637	0.71	0.79	62	CL, PEG
2	868	0.71	0.76	54	CL, CA, PEG
3	782	0.67	0.74	36	PEG, TRS, CL
4	339	0.65	0.81	48	PEG, MES
5	109	0.45	0.79	20	CL

Interfaces

17 interfaces between chains.

B–E · 1107 Å² buried · 22 hydrogen bonds · protein-protein
F–H · 1089 Å² buried · 22 hydrogen bonds · protein-protein
I–J · 1083 Å² buried · 23 hydrogen bonds · protein-protein
B–C · 1069 Å² buried · 22 hydrogen bonds · protein-protein
A–D · 1069 Å² buried · 24 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 disulfide (disulfide).

Compared structures

5WHU · Crystal structure of 3'SL bound ArtB · 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 Q404H3
Elsewhere: RCSB PDB 5WHU · PDBe 5WHU · UniProt Q404H3

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