Research workbench
Crystal structure of msba from salmonella typhimurium with amppnp, higher resolution form
Analyse Crystal structure of msba from salmonella typhimurium with amppnp, higher… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B60
- Type
- protein
- Length
- 2,288 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipid a export ATP-BINDING/PERMEASE protein msba
- EC
- 3.6.3.-
- UniProt
- P63359
- Ligands
- ANP
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 64% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Lipid a export ATP-BINDING/PERMEASE protein msba (EC 3.6.3.-) | protein | 572 | 64% helix, 10% strand | P63359 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 907 | 0.88 | 0.90 | 113 | ANP |
| 2 | 879 | 0.88 | 0.91 | 109 | ANP |
| 3 | 799 | 0.80 | 0.83 | 90 | empty |
| 4 | 735 | 0.79 | 0.83 | 71 | empty |
| 5 | 356 | 0.71 | 0.83 | 47 | empty |
Interfaces
3 interfaces between chains.
- C–D · 7224 Ų buried · 66 hydrogen bonds · protein-protein
- A–B · 7213 Ų buried · 63 hydrogen bonds · protein-protein
- A–C · 31 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3B60 · Crystal Structure of MsbA from Salmonella typhimurium with AMPPNP, higher resolution form · the same entry in another collection · chain D against D, TM-score 1.00
- P63359 · AlphaFold monomer V2.0 prediction for ATP-dependent lipid a-core flippase (P63359) · a predicted model of the same protein · chain A 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 P63359
- Elsewhere: RCSB PDB 3B60 · PDBe 3B60 · UniProt P63359
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