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Structure of human LAG3 domains 3-4 in complex with antibody single chain-variable fragment
Analyse Structure of human LAG3 domains 3-4 in complex with antibody single… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TZH
- Type
- protein
- Length
- 803 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SCFVF7; Lymphocyte activation gene 3 protein
- UniProt
- P18627
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | SCFVF7 | protein | 230 | 5% helix, 50% strand | — |
| D | Lymphocyte activation gene 3 protein | protein | 164 | 5% helix, 49% strand | P18627 |
| A | SCFVF7 | protein | 236 | 5% helix, 48% strand | — |
| B | Lymphocyte activation gene 3 protein | protein | 173 | 5% helix, 52% strand | P18627 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains D, B
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 | 589 | 0.70 | 0.79 | 76 | empty |
| 2 | 96 | 0.59 | 0.87 | 20 | empty |
| 3 | 78 | 0.52 | 0.85 | 18 | empty |
| 4 | 268 | 0.50 | 0.74 | 33 | empty |
| 5 | 70 | 0.40 | 0.80 | 18 | empty |
Interfaces
5 interfaces between chains.
- C–D · 824 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 802 Ų buried · 16 hydrogen bonds · protein-protein
- D–B · 274 Ų buried · 0 hydrogen bonds · protein-protein
- D–A · 135 Ų buried · 5 hydrogen bonds · protein-protein
- C–B · 120 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7TZH · Structure of human LAG3 domains 3-4 in complex with antibody single chain-variable… · the same entry in another collection · chain C against C, TM-score 1.00
- P18627 · AlphaFold monomer V2.0 prediction for lymphocyte activation gene 3 protein (P18627) · a predicted model of the same protein · chain D against A, TM-score 0.91
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 7TZH · PDBe 7TZH · UniProt P18627
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