Research workbench
Crystal structure of the pre-B cell receptor
Analyse Crystal structure of the pre-B cell receptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2H32
- Type
- protein
- Length
- 439 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin iota chain; Immunoglobulin omega chain; Immunoglobulin heavy chain
- UniProt
- P12018, P15814
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Immunoglobulin iota chain | protein | 111 | 8% helix, 48% strand | P12018 |
| B | Immunoglobulin omega chain | protein | 117 | 8% helix, 47% strand | P15814 |
| H | Immunoglobulin heavy chain | protein | 211 | 4% helix, 41% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 480 | 0.59 | 0.74 | 49 | empty |
| 2 | 64 | 0.42 | 0.81 | 14 | empty |
| 3 | 77 | 0.39 | 0.78 | 18 | empty |
| 4 | 57 | 0.27 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–H · 1235 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1106 Ų buried · 20 hydrogen bonds · protein-protein
- A–H · 705 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2H32 · Crystal structure of the pre-B cell receptor · the same entry in another collection · chain A against A, TM-score 1.00
- P12018 · AlphaFold monomer V2.0 prediction for immunoglobulin iota chain (P12018) · a predicted model of the same protein · chain A against A, TM-score 0.89
- 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 0.86
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 2H32 · PDBe 2H32 · UniProt P12018 · UniProt P15814
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