Research workbench
Mycobacterium smegmatis lpqy-sugabc complex in the catalytic intermediate state
Analyse Mycobacterium smegmatis lpqy-sugabc complex in the catalytic intermediate state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CAG
- Type
- protein
- Length
- 1,717 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacterial extracellular solute-binding protein; ABC sugar transporter, permease…
- UniProt
- A0R2C3, I7G6S2, A0R2C1, A0R2C0
- Ligands
- ATP, GLC, MG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 4 distinct chains · 38% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Bacterial extracellular solute-binding protein | protein | 435 | 32% helix, 8% strand | A0R2C3 |
| A | ABC sugar transporter, permease component | protein | 285 | 55% helix, 1% strand | I7G6S2 |
| B | ABC transporter, permease protein sugb | protein | 273 | 51% helix, 0% strand | A0R2C1 |
| C, D | ABC transporter, ATP-binding protein sugc | protein | 362 | 23% helix, 15% strand | A0R2C0 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains C, D
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains C, D
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1143 | 0.89 | 0.91 | 135 | GLC |
| 2 | 1151 | 0.81 | 0.82 | 82 | empty |
| 3 | 815 | 0.80 | 0.83 | 93 | MG, ATP |
| 4 | 933 | 0.77 | 0.80 | 92 | empty |
| 5 | 155 | 0.72 | 0.90 | 32 | empty |
Interfaces
8 interfaces between chains.
- A–B · 4393 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1605 Ų buried · 12 hydrogen bonds · protein-protein
- E–A · 1239 Ų buried · 6 hydrogen bonds · protein-protein
- E–B · 1110 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1073 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7CAG · Mycobacterium smegmatis LpqY-SugABC complex in the catalytic intermediate state · the same entry in another collection · chain E against E, 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 A0R2C3
- Every structure of UniProt I7G6S2
- Every structure of UniProt A0R2C1
- Every structure of UniProt A0R2C0
- Elsewhere: RCSB PDB 7CAG · PDBe 7CAG · UniProt A0R2C3 · UniProt I7G6S2 · UniProt A0R2C1 · UniProt A0R2C0
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