MolNFT v1 · #114319 · protein

Crystal structure of maltose binding protein in complex with a peristeric synthetic antibody

5BK2 · Maltose-binding periplasmic protein: “Crystal structure of maltose binding protein in complex with a peristeric synthetic antibody”. X-ray diffraction, 3 ligands (GLC, CL, PO4), 20 pockets (best druggability 0.73). MolNFT v1 #114319…

PDB: 5BK2
Type: protein
Length: 1,614 residues
Chains: 6
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
Ligands: GLC, CL, PO4
Pockets: 20 · best druggability 0.73

Structure

x-ray diffraction · 4 distinct chains · 22% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A	Maltose-binding periplasmic protein	protein	367	43% helix, 21% strand	P0AEX9
C	Sab heavy chain	protein	228	11% helix, 51% strand	—
H	Sab heavy chain	protein	220	13% helix, 51% strand	—
D, L	Sab light chain	protein	216	6% helix, 50% strand	—

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 4 copies · chains B, A
CL · Chloride ion · ion · 7 copies · chains B, A, C, H, D
PO4 · Phosphate ion · ion · 4 copies · chains C, H, D
GOL · Glycerol · additive · 11 copies · chains C, D, H, L

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	295	0.73	0.86	29	GLC
2	317	0.73	0.85	26	GLC
3	120	0.67	0.89	24	GOL
4	116	0.65	0.89	23	empty
5	309	0.58	0.77	31	GOL

Interfaces

7 interfaces between chains.

C–D · 1914 Å² buried · 8 hydrogen bonds · protein-protein
H–L · 1745 Å² buried · 9 hydrogen bonds · protein-protein
A–H · 723 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 705 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 583 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

5BK2 · Crystal structure of maltose binding protein in complex with a peristeric synthetic… · the same entry in another collection · chain B against B, 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
Elsewhere: RCSB PDB 5BK2 · PDBe 5BK2 · UniProt P0AEX9

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