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Crystal structure of an outward-facing mbp-maltose transporter complex bound to ADP-ALF4

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: 3PUW
Type: protein
Length: 1,881 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, ALF, UMQ, GLC, MG
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 5 distinct chains · 44% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	Maltose-binding periplasmic protein	protein	374	46% helix, 20% strand	P0AEX9
F	Maltose transport system permease protein malf	protein	490	53% helix, 16% strand	P02916
G	Maltose transport system permease protein malg	protein	288	68% helix, 3% strand	P68183
A	MALTOSE/MALTODEXTRIN import ATP-binding protein malk (EC 3.6.3.19)	protein	371	26% helix, 34% strand	P68187
B	MALTOSE/MALTODEXTRIN import ATP-binding protein malk (EC 3.6.3.19)	protein	358	27% 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
ALF · Tetrafluoroaluminate 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, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	811	0.84	0.86	81	empty
2	1200	0.80	0.82	109	MG, ADP, ALF
3	572	0.80	0.86	61	GLC
4	467	0.80	0.87	69	empty
5	232	0.73	0.88	38	empty

Interfaces

7 interfaces between chains.

F–G · 4032 Å² buried · 7 hydrogen bonds · protein-protein
E–F · 2134 Å² buried · 36 hydrogen bonds · protein-protein
A–B · 1932 Å² buried · 21 hydrogen bonds · protein-protein
E–G · 1130 Å² buried · 10 hydrogen bonds · protein-protein
G–A · 1047 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

3PUW · Crystal Structure of an outward-facing MBP-Maltose transporter complex bound to ADP-AlF4 · 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 0.92
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 3PUW · PDBe 3PUW · UniProt P0AEX9 · UniProt P02916 · UniProt P68183 · UniProt P68187

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