Research workbench
Crystal structure of a Fab in complex with a peptide derived from the LAG-3 D1 domain loop insertion
Analyse Crystal structure of a Fab in complex with a peptide derived from the LAG-3 D1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UM3
- Type
- protein
- Length
- 880 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3983
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Fab heavy chain; Fab light chain; D1 domain loop peptide from Lymphocyte activation gene…
- UniProt
- P18627
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.3983 · 5 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | Fab heavy chain | protein | 215 | 7% helix, 53% strand | — |
| M, L | Fab light chain | protein | 213 | 6% helix, 51% strand | — |
| H | Fab heavy chain | protein | 214 | 7% helix, 53% strand | — |
| B | D1 domain loop peptide from Lymphocyte activation gene 3 protein | protein | 12 | 0% helix, 0% strand | P18627 |
| A | D1 domain loop peptide from Lymphocyte activation gene 3 protein | protein | 13 | 0% helix, 0% strand | P18627 |
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 372 | 0.74 | 0.85 | 52 | empty |
| 2 | 346 | 0.73 | 0.85 | 44 | empty |
| 3 | 183 | 0.60 | 0.83 | 36 | empty |
| 4 | 231 | 0.60 | 0.80 | 36 | empty |
| 5 | 195 | 0.50 | 0.76 | 34 | empty |
Interfaces
9 interfaces between chains.
- H–L · 1808 Ų buried · 17 hydrogen bonds · protein-protein
- I–M · 1745 Ų buried · 13 hydrogen bonds · protein-protein
- I–H · 474 Ų buried · 6 hydrogen bonds · protein-protein
- M–B · 472 Ų buried · 6 hydrogen bonds · protein-protein
- L–A · 462 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- P18627 · AlphaFold monomer V2.0 prediction for lymphocyte activation gene 3 protein (P18627) · a predicted model of the same protein · chain B against A, TM-score 0.42
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 P18627
- Elsewhere: RCSB PDB 7UM3 · PDBe 7UM3 · UniProt P18627
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