MolNFT v1 · #190659 · protein
Structure of a membrane protein M3
7XT6 · B-cell antigen receptor complex-associated protein alpha…: “Structure of a membrane protein M3”. Electron microscopy, 3 ligands (NAG, BMA, MAN), 13 pockets (best druggability 0.80). MolNFT v1 #190659 on GenesisL1: 3D structure…
- PDB
- 7XT6
- Type
- protein
- Length
- 1,003 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- B-cell antigen receptor complex-associated protein alpha chain; Isoform 2 of…
- UniProt
- P11912, P40259
- Ligands
- NAG, BMA, MAN
- Pockets
- 13 · best druggability 0.80
Structure
electron microscopy · 4 distinct chains · 17% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | B-cell antigen receptor complex-associated protein alpha chain | protein | 137 | 21% helix, 25% strand | P11912 |
| B | Isoform 2 of immunoglobulin heavy constant mu | protein | 363 | 13% helix, 32% strand | — |
| C | B-cell antigen receptor complex-associated protein beta chain | protein | 139 | 24% helix, 29% strand | P40259 |
| D | Isoform 2 of immunoglobulin heavy constant mu | protein | 364 | 15% helix, 37% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains B, D, A, C
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains B, D
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 920 | 0.80 | 0.82 | 81 | empty |
| 2 | 357 | 0.66 | 0.80 | 38 | empty |
| 3 | 195 | 0.64 | 0.84 | 30 | empty |
| 4 | 335 | 0.61 | 0.78 | 53 | empty |
| 5 | 157 | 0.60 | 0.83 | 22 | empty |
Interfaces
6 interfaces between chains.
- B–D · 3007 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 1259 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1220 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 927 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 494 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 glycan, 10 disulfide (N-glycosylation, disulfide).
Compared structures
- 7XT6 · Structure of a membrane protein M3 · the same entry in another collection · chain A against A, 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 C against A, TM-score 0.73
- 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 0.65
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 P11912
- Every structure of UniProt P40259
- Elsewhere: RCSB PDB 7XT6 · PDBe 7XT6 · UniProt P11912 · UniProt P40259
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