Research workbench

A protein structure

Analyse A protein structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5L75
Type: protein
Length: 1,135 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lipopolysaccharide ABC transporter, ATP-binding protein lptb; FIG000988: predicted…
UniProt: W1B6A5, W1B830, W1B8C5
Ligands: PT
Pockets: 13 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 43% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lipopolysaccharide ABC transporter, ATP-binding protein lptb	protein	235	34% helix, 19% strand	W1B6A5
B	Lipopolysaccharide ABC transporter, ATP-binding protein lptb	protein	237	30% helix, 24% strand	W1B6A5
F	FIG000988: predicted permease	protein	323	51% helix, 7% strand	W1B830
G	FIG000906: predicted permease	protein	340	50% helix, 7% strand	W1B8C5

Ligands and binding sites

PT · Platinum (II) ion · metal · 2 copies · chains A, G

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

Pockets

13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	640	0.75	0.81	70	empty
2	908	0.73	0.77	68	empty
3	624	0.71	0.79	62	empty
4	476	0.67	0.78	58	empty
5	458	0.65	0.78	48	empty

Interfaces

4 interfaces between chains.

F–G · 1812 Å² buried · 12 hydrogen bonds · protein-protein
B–F · 1016 Å² buried · 9 hydrogen bonds · protein-protein
A–G · 996 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 618 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5L75 · A protein structure · 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 W1B6A5
Every structure of UniProt W1B830
Every structure of UniProt W1B8C5
Elsewhere: RCSB PDB 5L75 · PDBe 5L75 · UniProt W1B6A5 · UniProt W1B830 · UniProt W1B8C5

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