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Crystal structure of the maltose-binding PROTEIN/MALTOSE transporter complex in an pre-translocation conformation bound to maltoheptaose

Analyse Crystal structure of the maltose-binding PROTEIN/MALTOSE transporter complex in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4KHZ
Type: protein
Length: 1,873 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Maltose-binding periplasmic protein; Maltose transport system permease protein malf…
UniProt: P0AEX9, P02916, C9QV46, C9QV42
Ligands: PGV, GLC
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 5 distinct chains · 43% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	Maltose-binding periplasmic protein	protein	370	46% helix, 20% strand	P0AEX9
F	Maltose transport system permease protein malf	protein	483	53% helix, 14% strand	P02916
G	Binding-protein-dependent transport systems inner membrane component	protein	282	67% helix, 3% strand	C9QV46
A	Binding-protein-dependent transport systems inner membrane component	protein	370	26% helix, 33% strand	C9QV42
B	Binding-protein-dependent transport systems inner membrane component	protein	368	25% helix, 32% strand	C9QV42

Ligands and binding sites

PGV · (1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11E)-octadec-11-enoate · ligand · chains F, G
GLC · alpha-D-glucopyranose · sugar · 7 copies · chains E, G, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1143	0.87	0.88	105	GLC
2	739	0.87	0.90	86	empty
3	928	0.82	0.83	98	empty
4	297	0.81	0.92	30	GLC
5	599	0.74	0.81	47	PGV

Interfaces

7 interfaces between chains.

F–G · 3886 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1817 Å² buried · 22 hydrogen bonds · protein-protein
E–F · 1816 Å² buried · 19 hydrogen bonds · protein-protein
E–G · 1189 Å² buried · 11 hydrogen bonds · protein-protein
F–B · 782 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4KHZ · Crystal structure of the maltose-binding protein/maltose transporter complex in an… · the same entry in another collection · chain E against E, TM-score 1.00
P02916 · AlphaFold monomer V2.0 prediction for MALTOSE/MALTODEXTRIN transport system permease… · a predicted model of the same protein · chain F against A, TM-score 0.82

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 P02916
Every structure of UniProt C9QV46
Every structure of UniProt C9QV42
Elsewhere: RCSB PDB 4KHZ · PDBe 4KHZ · UniProt P0AEX9 · UniProt P02916 · UniProt C9QV46 · UniProt C9QV42

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