MolNFT v1 · #187182 · protein
Fab fragment bound to the cter peptide of LY6G6D
7S4G · Heavy chain Fab 1G4: “Fab fragment bound to the cter peptide of LY6G6D”. X-ray diffraction, 11 pockets (best druggability 0.78). MolNFT v1 #187182 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7S4G
- Type
- protein
- Length
- 1,743 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain Fab 1G4; Light chain Fab 1G4; Lymphocyte antigen 6 complex locus protein G6D
- UniProt
- O95868
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heavy chain Fab 1G4 | protein | 208 | 8% helix, 51% strand | — |
| B | Light chain Fab 1G4 | protein | 217 | 5% helix, 51% strand | — |
| C, H | Heavy chain Fab 1G4 | protein | 210 | 10% helix, 50% strand | — |
| D, F, L | Light chain Fab 1G4 | protein | 218 | 6% helix, 50% strand | — |
| E | Heavy chain Fab 1G4 | protein | 208 | 9% helix, 52% strand | — |
| G, I, J, K | Lymphocyte antigen 6 complex locus protein G6D | protein | 9 | 0% helix, 0% strand | O95868 |
Ligands and binding sites
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains A, B, C, D, E, F, H, L
- GOL · Glycerol · additive · 2 copies · chains D, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 594 | 0.78 | 0.84 | 84 | empty |
| 2 | 373 | 0.56 | 0.74 | 49 | empty |
| 3 | 342 | 0.53 | 0.74 | 47 | empty |
| 4 | 94 | 0.46 | 0.80 | 24 | empty |
| 5 | 147 | 0.42 | 0.75 | 19 | empty |
Interfaces
25 interfaces between chains.
- C–D · 1652 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1629 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1624 Ų buried · 16 hydrogen bonds · protein-protein
- H–L · 1609 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 342 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 7S4G · Fab fragment bound to the Cter peptide of Ly6G6D · the same entry in another collection · chain L against L, TM-score 1.00
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 O95868
- Elsewhere: RCSB PDB 7S4G · PDBe 7S4G · UniProt O95868
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