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Crystal structure of maltose bound mbp with a conformationally specific synthetic antigen binder (sab)

Analyse Crystal structure of maltose bound mbp with a conformationally specific… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3PGF
Type: protein
Length: 794 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Maltose-binding periplasmic protein; Sab heavy chain; Sab light chain
UniProt: P0AEX9, P0DOX5, Q8TCD0
Ligands: GLC
Pockets: 8 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 25% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Maltose-binding periplasmic protein	protein	358	46% helix, 18% strand	P0AEX9
H	Sab heavy chain	protein	222	8% helix, 50% strand	P0DOX5
L	Sab light chain	protein	214	6% helix, 51% strand	Q8TCD0

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
IMD · Imidazole · additive · 2 copies · chains A
GOL · Glycerol · additive · 2 copies · chains H, L

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

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	320	0.69	0.83	32	GLC, IMD
2	471	0.59	0.74	57	empty
3	199	0.57	0.80	33	empty
4	233	0.53	0.77	32	empty
5	141	0.50	0.79	22	empty

Interfaces

3 interfaces between chains.

H–L · 1846 Å² buried · 13 hydrogen bonds · protein-protein
A–H · 853 Å² buried · 12 hydrogen bonds · protein-protein
A–L · 384 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

3PGF · Crystal structure of maltose bound MBP with a conformationally specific synthetic antigen… · 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 P0AEX9
Every structure of UniProt P0DOX5
Every structure of UniProt Q8TCD0
Elsewhere: RCSB PDB 3PGF · PDBe 3PGF · UniProt P0AEX9 · UniProt P0DOX5 · UniProt Q8TCD0

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