Research workbench
Crystal structure of a Fab fragment bound to peptide ggm
Analyse Crystal structure of a Fab fragment bound to peptide ggm in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MFR
- Type
- protein
- Length
- 869 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody fragment - light chain of Fab; Antibody fragment - heavy chain of Fab…
- Ligands
- SO4
- Pockets
- 14 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, X | Antibody fragment - light chain of Fab | protein | 219 | 7% helix, 51% strand | — |
| B | Antibody fragment - heavy chain of Fab | protein | 214 | 7% helix, 50% strand | — |
| Y | Antibody fragment - heavy chain of Fab | protein | 211 | 4% helix, 53% strand | — |
| P, Q | Gly-gly-met | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains A, X, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 512 | 0.61 | 0.75 | 60 | empty |
| 2 | 460 | 0.59 | 0.75 | 53 | empty |
| 3 | 203 | 0.59 | 0.81 | 29 | SO4 |
| 4 | 315 | 0.58 | 0.77 | 30 | empty |
| 5 | 194 | 0.51 | 0.77 | 20 | SO4 |
Interfaces
7 interfaces between chains.
- A–B · 1877 Ų buried · 22 hydrogen bonds · protein-protein
- X–Y · 1815 Ų buried · 16 hydrogen bonds · protein-protein
- A–X · 879 Ų buried · 12 hydrogen bonds · protein-protein
- B–P · 224 Ų buried · 6 hydrogen bonds · protein-protein
- Y–Q · 217 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 7MFR · Crystal Structure of a Fab fragment bound to peptide GGM · the same entry in another collection · chain Q against Q, 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 7MFR · PDBe 7MFR
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