Research workbench
Crystal structure of heterosubtypic Fab S139/1
Analyse Crystal structure of heterosubtypic Fab S139/1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GMT
- Type
- protein
- Length
- 852 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab S139/1 light chain; Fab S139/1 heavy chain
- Ligands
- NAG, SO4
- Pockets
- 8 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, M | Fab S139/1 light chain | protein | 213 | 7% helix, 50% strand | — |
| H, I | Fab S139/1 heavy chain | protein | 213 | 3% helix, 53% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains H, I
- SO4 · Sulfate ion · ion · 2 copies · chains L, H, M, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 305 | 0.57 | 0.76 | 35 | SO4 |
| 2 | 320 | 0.53 | 0.74 | 43 | SO4 |
| 3 | 100 | 0.39 | 0.76 | 22 | empty |
| 4 | 139 | 0.38 | 0.73 | 23 | empty |
| 5 | 99 | 0.36 | 0.74 | 22 | empty |
Interfaces
3 interfaces between chains.
- M–I · 1854 Ų buried · 17 hydrogen bonds · protein-protein
- L–H · 1841 Ų buried · 10 hydrogen bonds · protein-protein
- H–M · 115 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan, 2 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 4GMT · Crystal structure of heterosubtypic Fab S139/1 · 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
- Elsewhere: RCSB PDB 4GMT · PDBe 4GMT
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