Research workbench
Cryo-EM structure of human secretory immunoglobulin a in complex with the N-terminal domain of spsa
Analyse Cryo-EM structure of human secretory immunoglobulin a in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LXW
- Type
- protein
- Length
- 1,595 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-2,IMMUNOGLOBULIN heavy constant alpha 1; Immunoglobulin J chain; Polymeric…
- UniProt
- P60568, P01876, P01591, P01833, O33753
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 7 distinct chains · 7% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-2,IMMUNOGLOBULIN heavy constant alpha 1 | protein | 225 | 7% helix, 41% strand | P60568, P01876 |
| B | Interleukin-2,IMMUNOGLOBULIN heavy constant alpha 1 | protein | 218 | 5% helix, 38% strand | P60568, P01876 |
| C | Interleukin-2,IMMUNOGLOBULIN heavy constant alpha 1 | protein | 221 | 7% helix, 38% strand | P60568, P01876 |
| D | Interleukin-2,IMMUNOGLOBULIN heavy constant alpha 1 | protein | 229 | 9% helix, 41% strand | P60568, P01876 |
| J | Immunoglobulin J chain | protein | 128 | 2% helix, 34% strand | P01591 |
| P | Polymeric immunoglobulin receptor | protein | 513 | 2% helix, 43% strand | P01833 |
| S | Siga binding protein | protein | 61 | 54% helix, 0% strand | O33753 |
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1028 | 0.83 | 0.84 | 80 | empty |
| 2 | 662 | 0.76 | 0.81 | 52 | empty |
| 3 | 895 | 0.71 | 0.76 | 77 | empty |
| 4 | 358 | 0.64 | 0.79 | 36 | empty |
| 5 | 114 | 0.54 | 0.83 | 29 | empty |
Interfaces
15 interfaces between chains.
- D–J · 1998 Ų buried · 29 hydrogen bonds · protein-protein
- A–J · 1716 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1676 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1598 Ų buried · 18 hydrogen bonds · protein-protein
- P–S · 953 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 disulfide (disulfide).
Compared structures
- 6LXW · Cryo-EM structure of human secretory immunoglobulin A in complex with the N-terminal… · the same entry in another collection · chain A against A, TM-score 1.00
- P01833 · AlphaFold monomer V2.0 prediction for polymeric immunoglobulin receptor (P01833) · a predicted model of the same protein · chain P against A, TM-score 0.98
- P01591 · AlphaFold monomer V2.0 prediction for immunoglobulin J chain (P01591) · a predicted model of the same protein · chain J against A, TM-score 0.94
- P01876 · AlphaFold monomer V2.0 prediction for immunoglobulin heavy constant alpha 1 (P01876) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 P60568
- Every structure of UniProt P01876
- Every structure of UniProt P01591
- Every structure of UniProt P01833
- Every structure of UniProt O33753
- Elsewhere: RCSB PDB 6LXW · PDBe 6LXW · UniProt P60568 · UniProt P01876 · UniProt P01591 · UniProt P01833 · UniProt O33753
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