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Crystal structure of the maltose-binding PROTEIN/MALTOSE transporter complex in an outward-facing conformation bound to mgamppnp
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
- 3RLF
- Type
- protein
- Length
- 1,891 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, ANP, UMQ, GLC, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Maltose-binding periplasmic protein | protein | 374 | 44% helix, 18% strand | P0AEX9 |
| F | Maltose transport system permease protein malf | protein | 490 | 53% helix, 15% strand | P02916 |
| G | Maltose transport system permease protein malg | protein | 286 | 66% helix, 3% strand | P68183 |
| A | MALTOSE/MALTODEXTRIN import ATP-binding protein malk (EC 3.6.3.19) | protein | 371 | 27% helix, 33% strand | P68187 |
| B | MALTOSE/MALTODEXTRIN import ATP-binding protein malk (EC 3.6.3.19) | protein | 370 | 26% helix, 31% 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 · 4 copies · chains F, G
- ANP · Phosphoaminophosphonic acid-adenylate ester · 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 997 | 0.87 | 0.88 | 136 | empty |
| 2 | 1045 | 0.84 | 0.85 | 113 | empty |
| 3 | 904 | 0.82 | 0.84 | 73 | GLC |
| 4 | 1149 | 0.82 | 0.83 | 121 | MG, ANP |
| 5 | 571 | 0.69 | 0.78 | 74 | empty |
Interfaces
7 interfaces between chains.
- F–G · 4041 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 2109 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 1928 Ų buried · 23 hydrogen bonds · protein-protein
- E–G · 1134 Ų buried · 12 hydrogen bonds · protein-protein
- G–A · 1032 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3RLF · Crystal structure of the maltose-binding protein/maltose transporter complex in an… · the same entry in another collection · chain B against B, 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 A 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 0.93
- 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 0.79
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 3RLF · PDBe 3RLF · UniProt P0AEX9 · UniProt P02916 · UniProt P68183 · UniProt P68187
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