Research workbench
Crystal structure of a surrogate light chain (LAMBDA5 and vpreb) homodimer
Analyse Crystal structure of a surrogate light chain (LAMBDA5 and vpreb) homodimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2H3N
- Type
- protein
- Length
- 426 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vpreb protein; Ig lambda-5
- UniProt
- P12018, P15814
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vpreb protein | protein | 99 | 6% helix, 53% strand | P12018 |
| B | Ig lambda-5 | protein | 116 | 9% helix, 52% strand | P15814 |
| C | Vpreb protein | protein | 99 | 9% helix, 51% strand | P12018 |
| D | Ig lambda-5 | protein | 112 | 10% helix, 51% strand | P15814 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.58 | 0.74 | 54 | empty |
| 2 | 53 | 0.54 | 0.89 | 16 | empty |
| 3 | 120 | 0.42 | 0.76 | 24 | empty |
| 4 | 73 | 0.32 | 0.75 | 20 | empty |
| 5 | 53 | 0.29 | 0.75 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1154 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1093 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 929 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 261 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 259 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2H3N · Crystal structure of a surrogate light chain (LAMBDA5 and VpreB) homodimer · the same entry in another collection · chain D against D, TM-score 1.00
- P12018 · AlphaFold monomer V2.0 prediction for immunoglobulin iota chain (P12018) · a predicted model of the same protein · chain C against A, TM-score 0.97
- P15814 · AlphaFold monomer V2.0 prediction for immunoglobulin lambda-like polypeptide 1 (P15814) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P12018
- Every structure of UniProt P15814
- Elsewhere: RCSB PDB 2H3N · PDBe 2H3N · UniProt P12018 · UniProt P15814
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