Research workbench
Bence jones kwr protein- immunoglobulin light chain dimer, P3(1)21 crystal form
Analyse Bence jones kwr protein- immunoglobulin light chain dimer, P3(1)21 crystal form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OMB
- Type
- protein
- Length
- 868 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bence jones kwr protein - immunoglobulin light chain
- Ligands
- IPH, SO4
- Pockets
- 14 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Bence jones kwr protein - immunoglobulin light chain | protein | 217 | 6% helix, 47% strand | — |
Ligands and binding sites
- IPH · Phenol · ligand · 2 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.73 | 0.97 | 10 | IPH |
| 2 | 67 | 0.71 | 0.95 | 12 | IPH |
| 3 | 986 | 0.70 | 0.75 | 105 | empty |
| 4 | 508 | 0.65 | 0.77 | 53 | empty |
| 5 | 272 | 0.62 | 0.80 | 43 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1851 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1746 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 739 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 4 modified (disulfide, cyclization).
Compared structures
- 2OMB · Bence Jones KWR Protein- Immunoglobulin Light Chain Dimer, P3(1)21 Crystal Form · 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
- Elsewhere: RCSB PDB 2OMB · PDBe 2OMB
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