MolNFT v1 · #119895 · protein
Crystal structure of a Fab fragment with its ligand peptide
5GIS · Heavy chain of Fab fragment: “Crystal structure of a Fab fragment with its ligand peptide”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.66). MolNFT v1 #119895 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5GIS
- Type
- protein
- Length
- 432 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain of Fab fragment; Light chain of Fab fragment…
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Heavy chain of Fab fragment | protein | 211 | 9% helix, 51% strand | — |
| L | Light chain of Fab fragment | protein | 211 | 5% helix, 52% strand | — |
| C | Thr-lys-pro-ile-thr-ile-gly-ser-his-ala-his-gly-asp-gln- tyr-lys | protein | 10 | 40% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 640 | 0.66 | 0.76 | 60 | empty |
| 2 | 69 | 0.33 | 0.75 | 16 | empty |
| 3 | 64 | 0.28 | 0.73 | 19 | empty |
| 4 | 57 | 0.28 | 0.74 | 13 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1649 Ų buried · 14 hydrogen bonds · protein-protein
- H–C · 393 Ų buried · 7 hydrogen bonds · protein-protein
- L–C · 308 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 5GIS · Crystal structure of a Fab fragment with its ligand peptide · the same entry in another collection · chain H against H, 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 5GIS · PDBe 5GIS
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