MolNFT v1 · #156941 · protein
LPTB(E163Q)FGC from vibrio cholerae
6MJP · ABC transporter ATP-binding protein: “LPTB(E163Q)FGC from vibrio cholerae”. X-ray diffraction, 5 ligands (AE3, JU7, MA4), 12 pockets (best druggability 0.76). MolNFT v1 #156941 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6MJP
- Type
- protein
- Length
- 1,349 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC transporter ATP-binding protein; Lipopolysaccharide export system protein lptc…
- EC
- 3.6.3.-
- UniProt
- O30650, A0A085S5D1, A0A0F0BAF3, A0A0H6JG76
- Ligands
- AE3, JU7, MA4, CA, CL
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ABC transporter ATP-binding protein (EC 3.6.3.-) | protein | 240 | 39% helix, 25% strand | O30650 |
| C | Lipopolysaccharide export system protein lptc | protein | 174 | 16% helix, 45% strand | A0A085S5D1 |
| F | FIG000988: predicted permease | protein | 341 | 59% helix, 13% strand | A0A0F0BAF3 |
| G | Lps export ABC transporter permease lptg | protein | 354 | 61% helix, 18% strand | A0A0H6JG76 |
Ligands and binding sites
- AE3 · 2-(2-ethoxyethoxy)ethanol · ligand · 2 copies · chains A
- JU7 · 6-cyclohexylhexyl beta-D-glucopyranoside · ligand · chains B, F
- MA4 · Cyclohexyl-hexyl-beta-D-maltoside · ligand · chains F, G
- CA · Calcium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains B, G
- LMT · Dodecyl-beta-D-maltoside · additive · 3 copies · chains C, F, G, A
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, G, B
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 364 | 0.76 | 0.86 | 57 | empty |
| 2 | 901 | 0.73 | 0.76 | 73 | LMT |
| 3 | 447 | 0.72 | 0.82 | 53 | CA, CL |
| 4 | 836 | 0.70 | 0.75 | 83 | PEG, GOL, LMT |
| 5 | 497 | 0.64 | 0.76 | 54 | empty |
Interfaces
6 interfaces between chains.
- C–F · 1556 Ų buried · 14 hydrogen bonds · protein-protein
- B–F · 1113 Ų buried · 5 hydrogen bonds · protein-protein
- F–G · 1103 Ų buried · 3 hydrogen bonds · protein-protein
- A–G · 945 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 738 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6MJP · LptB(E163Q)FGC from Vibrio cholerae · the same entry in another collection · chain A against A, 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 O30650
- Every structure of UniProt A0A085S5D1
- Every structure of UniProt A0A0F0BAF3
- Every structure of UniProt A0A0H6JG76
- Elsewhere: RCSB PDB 6MJP · PDBe 6MJP · UniProt O30650 · UniProt A0A085S5D1 · UniProt A0A0F0BAF3 · UniProt A0A0H6JG76
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