Research workbench
Structure of S. aureus protein a bound to a human IgM Fab
Analyse Structure of S. aureus protein a bound to a human IgM Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DEE
- Type
- protein
- Length
- 1,416 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IgM rf 2A2; Immunoglobulin G binding protein a
- UniProt
- P02976
- Pockets
- 20 · best druggability 0.58
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | IgM rf 2A2 | protein | 214 | 6% helix, 51% strand | — |
| B, D, F | IgM rf 2A2 | protein | 223 | 3% helix, 52% strand | — |
| G | Immunoglobulin G binding protein a | protein | 51 | 78% helix, 0% strand | P02976 |
| H | Immunoglobulin G binding protein a | protein | 54 | 76% helix, 0% strand | P02976 |
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 447 | 0.58 | 0.74 | 58 | empty |
| 2 | 225 | 0.57 | 0.79 | 34 | empty |
| 3 | 185 | 0.57 | 0.80 | 27 | empty |
| 4 | 342 | 0.56 | 0.75 | 46 | empty |
| 5 | 334 | 0.54 | 0.74 | 45 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2013 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 1999 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1944 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 694 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 641 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide (disulfide).
Compared structures
- 1DEE · Structure of S. aureus protein A bound to a human IgM Fab · the same entry in another collection · chain H against H, TM-score 1.00
- P02976 · AlphaFold monomer V2.0 prediction for immunoglobulin G-binding protein a (P02976) · a predicted model of the same protein · chain G against A, TM-score 0.95
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 P02976
- Elsewhere: RCSB PDB 1DEE · PDBe 1DEE · UniProt P02976
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