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Crystal structure of an outward-facing mbp-maltose transporter complex bound to ADP-BEF3

Analyse Crystal structure of an outward-facing mbp-maltose transporter complex bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3PUX
Type: protein
Length: 1,886 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…
EC: 3.6.3.19
UniProt: P0AEX9, P02916, P68183, P68187
Ligands: PGV, ADP, BEF, UMQ, GLC, MG
Pockets: 20 · best druggability 0.83

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	374	45% helix, 20% strand	P0AEX9
F	Maltose transport system permease protein malf	protein	490	52% helix, 16% strand	P02916
G	Maltose transport system permease protein malg	protein	293	66% helix, 3% strand	P68183
A	MALTOSE/MALTODEXTRIN import ATP-binding protein malk (EC 3.6.3.19)	protein	371	28% helix, 34% strand	P68187
B	MALTOSE/MALTODEXTRIN import ATP-binding protein malk (EC 3.6.3.19)	protein	358	25% helix, 32% strand	P68187

Ligands and binding sites

PGV · (1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11E)-octadec-11-enoate · ligand · 10 copies · chains F, G
ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
BEF · Beryllium trifluoride ion · ligand · 2 copies · chains A, B
UMQ · Undecyl-maltoside · ligand · chains E, F
GLC · alpha-D-glucopyranose · sugar · 2 copies · chains F
MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	759	0.83	0.87	78	empty
2	653	0.83	0.88	93	empty
3	886	0.82	0.84	74	GLC
4	1186	0.81	0.82	113	MG, ADP, BEF
5	714	0.75	0.80	48	PGV

Interfaces

7 interfaces between chains.

F–G · 4140 Å² buried · 8 hydrogen bonds · protein-protein
E–F · 2111 Å² buried · 37 hydrogen bonds · protein-protein
A–B · 1953 Å² buried · 25 hydrogen bonds · protein-protein
E–G · 1106 Å² buried · 12 hydrogen bonds · protein-protein
G–A · 1042 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

3PUX · Crystal Structure of an outward-facing MBP-Maltose transporter complex bound to ADP-BeF3 · the same entry in another collection · chain A against A, TM-score 1.00
P68187 · AlphaFold monomer V2.0 prediction for MALTOSE/MALTODEXTRIN import ATP-binding protein… · a predicted model of the same protein · chain B against A, TM-score 0.98
P68183 · AlphaFold monomer V2.0 prediction for MALTOSE/MALTODEXTRIN transport system permease… · a predicted model of the same protein · chain G against A, TM-score 0.91
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 0.78

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 P68183
Every structure of UniProt P68187
Elsewhere: RCSB PDB 3PUX · PDBe 3PUX · UniProt P0AEX9 · UniProt P02916 · UniProt P68183 · UniProt P68187

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