Research workbench
Structure of human B-cell antigen receptor of the IgM isotype
Analyse Structure of human B-cell antigen receptor of the IgM isotype in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XQ8
- Type
- protein
- Length
- 1,889 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chimera of heavy chain of VRC01 antibody Fab and isoform 2 of immunoglobulin heavy…
- UniProt
- P01834, P11912, P40259
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 4 distinct chains · 14% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, v | Chimera of heavy chain of VRC01 antibody Fab and isoform 2 of immunoglobulin heavy constant mu | protein | 595 | 11% helix, 44% strand | — |
| L, R | Light chain of Fab fragments of the VRC01 antibody, immunoglobulin kappa constant | protein | 210 | 4% helix, 44% strand | P01834 |
| A | B-cell antigen receptor complex-associated protein alpha chain | protein | 139 | 27% helix, 20% strand | P11912 |
| B | B-cell antigen receptor complex-associated protein beta chain | protein | 140 | 27% helix, 24% strand | P40259 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains C, v, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 955 | 0.81 | 0.83 | 89 | empty |
| 2 | 953 | 0.78 | 0.81 | 125 | empty |
| 3 | 1149 | 0.78 | 0.80 | 128 | empty |
| 4 | 627 | 0.77 | 0.83 | 89 | empty |
| 5 | 622 | 0.76 | 0.83 | 80 | empty |
Interfaces
8 interfaces between chains.
- C–v · 3349 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1442 Ų buried · 11 hydrogen bonds · protein-protein
- v–A · 1387 Ų buried · 10 hydrogen bonds · protein-protein
- v–B · 996 Ų buried · 16 hydrogen bonds · protein-protein
- C–L · 740 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 14 glycan, 11 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 7XQ8 · Structure of human B-cell antigen receptor of the IgM isotype · the same entry in another collection · chain B against B, TM-score 1.00
- P40259 · AlphaFold monomer V2.0 prediction for B-cell antigen receptor complex-associated protein… · a predicted model of the same protein · chain B against A, TM-score 0.72
- P11912 · AlphaFold monomer V2.0 prediction for B-cell antigen receptor complex-associated protein… · a predicted model of the same protein · chain A against A, TM-score 0.67
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 P01834
- Every structure of UniProt P11912
- Every structure of UniProt P40259
- Elsewhere: RCSB PDB 7XQ8 · PDBe 7XQ8 · UniProt P01834 · UniProt P11912 · UniProt P40259
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