Research workbench
Crystal structure of lipopolysaccharide binding protein
Analyse Crystal structure of lipopolysaccharide binding protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M4D
- Type
- protein
- Length
- 890 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipopolysaccharide-binding protein
- UniProt
- Q61805
- Ligands
- PC1, NAG
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipopolysaccharide-binding protein | protein | 448 | 20% helix, 45% strand | Q61805 |
| B | Lipopolysaccharide-binding protein | protein | 442 | 20% helix, 42% strand | Q61805 |
Ligands and binding sites
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 562 | 0.86 | 0.91 | 50 | PC1 |
| 2 | 583 | 0.85 | 0.89 | 51 | PC1 |
| 3 | 759 | 0.83 | 0.85 | 82 | empty |
| 4 | 591 | 0.72 | 0.79 | 56 | empty |
| 5 | 419 | 0.63 | 0.78 | 45 | empty |
Interfaces
1 interface between chains.
- A–B · 830 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4M4D · Crystal structure of lipopolysaccharide binding protein · the same entry in another collection · chain A against A, TM-score 1.00
- Q61805 · AlphaFold monomer V2.0 prediction for lipopolysaccharide-binding protein (Q61805) · a predicted model of the same protein · chain B against A, TM-score 0.82
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 Q61805
- Elsewhere: RCSB PDB 4M4D · PDBe 4M4D · UniProt Q61805
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