Research workbench
Crystal structure of MOR04357, a neutralizing anti-human gm-csf antibody Fab fragment
Analyse Crystal structure of MOR04357, a neutralizing anti-human gm-csf antibody Fab… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D7S
- Type
- protein
- Length
- 423 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunglobulin G1 Fab fragment, light chain; Immunglobulin G1 Fab fragment, heavy chain
- Ligands
- BUD
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Immunglobulin G1 Fab fragment, light chain | protein | 205 | 8% helix, 49% strand | — |
| H | Immunglobulin G1 Fab fragment, heavy chain | protein | 218 | 8% helix, 50% strand | — |
Ligands and binding sites
- BUD · (2S,3S)-butane-2,3-diol · ligand · 2 copies · chains L, H
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 | 401 | 0.58 | 0.75 | 45 | empty |
| 2 | 218 | 0.48 | 0.74 | 28 | empty |
| 3 | 75 | 0.43 | 0.80 | 17 | BUD |
| 4 | 67 | 0.38 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- L–H · 1651 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5D7S · Crystal structure of MOR04357, a neutralizing anti-human GM-CSF antibody Fab fragment · 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 5D7S · PDBe 5D7S
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