Research workbench
Integrin ALPHAM/BETA2 ectodomain in complex with adenylate cyclase toxin RTX751 and M1F5 Fab
Analyse Integrin ALPHAM/BETA2 ectodomain in complex with adenylate cyclase toxin RTX751… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7USL
- Type
- protein
- Length
- 2,464 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha-M; Integrin beta; Bifunctional hemolysin-adenylate cyclase; M1F5 Fab heavy…
- UniProt
- P11215, A0A494C0X7, A5JW88
- Ligands
- NAG, FUC, CA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 5 distinct chains · 8% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha-M | protein | 856 | 4% helix, 49% strand | P11215 |
| B | Integrin beta | protein | 673 | 19% helix, 27% strand | A0A494C0X7 |
| C | Bifunctional hemolysin-adenylate cyclase | protein | 715 | 4% helix, 37% strand | A5JW88 |
| H | M1F5 Fab heavy chain | protein | 114 | 11% helix, 45% strand | — |
| L | M1F5 Fab light chain | protein | 106 | 0% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, C, B
- FUC · alpha-L-fucopyranose · sugar · chains A, C
- CA · Calcium ion · metal · 33 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 694 | 0.85 | 0.88 | 74 | empty |
| 2 | 1190 | 0.74 | 0.77 | 98 | empty |
| 3 | 254 | 0.72 | 0.87 | 35 | empty |
| 4 | 185 | 0.68 | 0.87 | 35 | empty |
| 5 | 454 | 0.63 | 0.76 | 42 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2582 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1581 Ų buried · 14 hydrogen bonds · protein-protein
- H–L · 765 Ų buried · 5 hydrogen bonds · protein-protein
- C–H · 748 Ų buried · 8 hydrogen bonds · protein-protein
- C–L · 361 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 37 disulfide, 13 glycan (disulfide, N-glycosylation).
Compared structures
- 7USL · Integrin alphaM/beta2 ectodomain in complex with adenylate cyclase toxin RTX751 and M1F5… · the same entry in another collection · chain A against A, TM-score 1.00
- P11215 · AlphaFold monomer V2.0 prediction for integrin alpha-M (P11215) · a predicted model of the same protein · chain A against A, TM-score 0.66
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 P11215
- Every structure of UniProt A0A494C0X7
- Every structure of UniProt A5JW88
- Elsewhere: RCSB PDB 7USL · PDBe 7USL · UniProt P11215 · UniProt A0A494C0X7 · UniProt A5JW88
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