Research workbench
The structure of bovine beta-lactoglobulin in novel crystals grown at pH 3.8
Analyse The structure of bovine beta-lactoglobulin in novel crystals grown at pH 3.8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NKQ
- Type
- protein
- Length
- 954 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactoglobulin
- UniProt
- P02754
- Ligands
- CA
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Beta-lactoglobulin | protein | 160 | 17% helix, 40% strand | P02754 |
| C, E | Beta-lactoglobulin | protein | 159 | 17% helix, 40% strand | P02754 |
| D, F | Beta-lactoglobulin | protein | 159 | 17% helix, 40% strand | P02754 |
| A | Beta-lactoglobulin | protein | 158 | 17% helix, 41% strand | P02754 |
Ligands and binding sites
- CA · Calcium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 906 | 0.85 | 0.87 | 91 | empty |
| 2 | 591 | 0.79 | 0.85 | 54 | empty |
| 3 | 492 | 0.76 | 0.84 | 61 | empty |
| 4 | 59 | 0.73 | 0.98 | 22 | empty |
| 5 | 50 | 0.73 | 0.99 | 20 | empty |
Interfaces
11 interfaces between chains.
- C–D · 552 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 520 Ų buried · 9 hydrogen bonds · protein-protein
- B–A · 512 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 492 Ų buried · 4 hydrogen bonds · protein-protein
- B–F · 465 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6NKQ · The structure of bovine beta-lactoglobulin in novel crystals grown at pH 3.8 · the same entry in another collection · chain B against B, 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 P02754
- Elsewhere: RCSB PDB 6NKQ · PDBe 6NKQ · UniProt P02754
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