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Crystal structure of a LACY/NANOBODY complex

Analyse Crystal structure of a LACY/NANOBODY complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5GXB
Type: protein
Length: 519 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lactose permease; Nanobody
UniProt: P02920
Pockets: 1 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 60% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lactose permease	protein	387	79% helix, 0% strand	P02920
B	Nanobody	protein	132	7% helix, 39% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1116	0.83	0.83	70	empty

Interfaces

1 interface between chains.

A–B · 1043 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5GXB · crystal structure of a LacY/Nanobody complex · the same entry in another collection · chain A against A, TM-score 1.00
P02920 · AlphaFold monomer V2.0 prediction for lactose permease (P02920) · a predicted model of the same protein · chain A against A, TM-score 0.80

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 P02920
Elsewhere: RCSB PDB 5GXB · PDBe 5GXB · UniProt P02920

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