Research workbench
Integrin I domain of complement receptor 3 in complex with C3D
Analyse Integrin I domain of complement receptor 3 in complex with C3D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M76
- Type
- protein
- Length
- 475 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C3; Integrin alpha-M
- UniProt
- P01024, P11215
- Ligands
- NI
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C3 | protein | 296 | 57% helix, 2% strand | P01024 |
| B | Integrin alpha-M | protein | 179 | 37% helix, 22% strand | P11215 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.58 | 0.83 | 19 | empty |
| 2 | 216 | 0.53 | 0.78 | 27 | empty |
| 3 | 96 | 0.43 | 0.78 | 17 | empty |
| 4 | 111 | 0.39 | 0.75 | 21 | empty |
| 5 | 53 | 0.32 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 560 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4M76 · Integrin I domain of complement receptor 3 in complex with C3d · 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 B against A, TM-score 0.95
- P01024 · AlphaFold monomer V2.0 prediction for complement C3 (P01024) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 P01024
- Every structure of UniProt P11215
- Elsewhere: RCSB PDB 4M76 · PDBe 4M76 · UniProt P01024 · UniProt P11215
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