MolNFT v1 · #174911 · protein
Mycobacterium smegmatis lpqy-sugabc complex in the pre-translocation state
7CAF · Bacterial extracellular solute-binding protein: “Mycobacterium smegmatis lpqy-sugabc complex in the pre-translocation state”. Electron microscopy, 1 ligand (GLC), 20 pockets (best druggability 0.87). MolNFT v1 #174911 on GenesisL1…
- PDB
- 7CAF
- Type
- protein
- Length
- 1,767 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacterial extracellular solute-binding protein; ABC transporter, ATP-binding protein…
- UniProt
- A0R2C3, A0R2C0, I7G6S2, A0R2C1
- Ligands
- GLC
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 45% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Bacterial extracellular solute-binding protein | protein | 443 | 38% helix, 10% strand | A0R2C3 |
| C, D | ABC transporter, ATP-binding protein sugc | protein | 384 | 27% helix, 22% strand | A0R2C0 |
| A | ABC sugar transporter, permease component | protein | 284 | 66% helix, 1% strand | I7G6S2 |
| B | ABC transporter, permease protein sugb | protein | 272 | 63% helix, 0% strand | A0R2C1 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 980 | 0.87 | 0.88 | 126 | empty |
| 2 | 1196 | 0.86 | 0.87 | 94 | GLC |
| 3 | 258 | 0.84 | 0.96 | 40 | empty |
| 4 | 543 | 0.73 | 0.81 | 60 | empty |
| 5 | 337 | 0.71 | 0.83 | 48 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4184 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1358 Ų buried · 6 hydrogen bonds · protein-protein
- E–A · 1123 Ų buried · 8 hydrogen bonds · protein-protein
- E–B · 987 Ų buried · 12 hydrogen bonds · protein-protein
- D–A · 772 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7CAF · Mycobacterium smegmatis LpqY-SugABC complex in the pre-translocation 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 A0R2C0
- Every structure of UniProt I7G6S2
- Every structure of UniProt A0R2C1
- Elsewhere: RCSB PDB 7CAF · PDBe 7CAF · UniProt A0R2C3 · UniProt A0R2C0 · UniProt I7G6S2 · UniProt A0R2C1
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