Research workbench
Crystal structure of a chimeric ALPHA1 integrin I-domain in complex with the Fab fragment of a humanized neutralizing antibody
Analyse Crystal structure of a chimeric ALPHA1 integrin I-domain 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
- 1MHP
- Type
- protein
- Length
- 1,030 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Integrin alpha 1, (residues 169-360); Fab fragment, heavy chain; Fab fragment, light chain
- UniProt
- P18614
- Ligands
- MN
- Pockets
- 9 · best druggability 0.61
Structure
x-ray diffraction · 6 distinct chains · 18% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Integrin alpha 1, (residues 169-360) | protein | 184 | 39% helix, 23% strand | P18614 |
| H | Fab fragment, heavy chain | protein | 219 | 9% helix, 54% strand | — |
| L | Fab fragment, light chain | protein | 212 | 4% helix, 51% strand | — |
| B | Integrin alpha 1, (residues 169-360) | protein | 192 | 41% helix, 22% strand | P18614 |
| X | Fab fragment, heavy chain | protein | 118 | 5% helix, 53% strand | — |
| Y | Fab fragment, light chain | protein | 105 | 0% helix, 50% strand | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, H, B, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.61 | 0.80 | 32 | empty |
| 2 | 57 | 0.61 | 0.92 | 18 | empty |
| 3 | 253 | 0.52 | 0.76 | 38 | empty |
| 4 | 113 | 0.48 | 0.80 | 22 | empty |
| 5 | 179 | 0.47 | 0.76 | 27 | empty |
Interfaces
8 interfaces between chains.
- H–L · 1960 Ų buried · 16 hydrogen bonds · protein-protein
- X–Y · 754 Ų buried · 8 hydrogen bonds · protein-protein
- B–X · 701 Ų buried · 10 hydrogen bonds · protein-protein
- A–H · 506 Ų buried · 11 hydrogen bonds · protein-protein
- B–Y · 452 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1MHP · Crystal structure of a chimeric alpha1 integrin I-domain in complex with the Fab fragment… · the same entry in another collection · chain Y against Y, TM-score 1.00
- P18614 · AlphaFold monomer V2.0 prediction for integrin alpha-1 (P18614) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P18614
- Elsewhere: RCSB PDB 1MHP · PDBe 1MHP · UniProt P18614
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