MolNFT v1 · #188592 · protein
Structure of human LAG3 in complex with antibody single-chain variable fragment
7TZG · SCFVF7: “Structure of human LAG3 in complex with antibody single-chain variable fragment”. X-ray diffraction, 1 ligand (NAG), 11 pockets (best druggability 0.71). MolNFT v1 #188592 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7TZG
- Type
- protein
- Length
- 1,195 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
- 11 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 3% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SCFVF7 | protein | 234 | 4% helix, 44% strand | — |
| B | SCFVF7 | protein | 234 | 3% helix, 51% strand | — |
| C | Lymphocyte activation gene 3 protein | protein | 354 | 3% helix, 38% strand | P18627 |
| D | Lymphocyte activation gene 3 protein | protein | 373 | 1% helix, 32% strand | P18627 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 500 | 0.71 | 0.81 | 63 | empty |
| 2 | 532 | 0.69 | 0.79 | 64 | empty |
| 3 | 508 | 0.68 | 0.79 | 64 | empty |
| 4 | 500 | 0.66 | 0.78 | 63 | empty |
| 5 | 285 | 0.58 | 0.78 | 45 | empty |
Interfaces
3 interfaces between chains.
- A–D · 852 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 821 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 552 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 7TZG · Structure of human LAG3 in complex with antibody single-chain variable fragment · the same entry in another collection · chain A against A, 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 C against A, TM-score 0.82
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 7TZG · PDBe 7TZG · UniProt P18627
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