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Crystal structure of MOR04302, a neutralizing anti-human gm-csf antibody Fab fragment in complex with human gm-csf
Analyse Crystal structure of MOR04302, 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
- 5D71
- Type
- protein
- Length
- 523 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Granulocyte-macrophage colony-stimulating factor; Immunglobulin G1 Fab fragment, heavy…
- UniProt
- P04141
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Granulocyte-macrophage colony-stimulating factor | protein | 114 | 48% helix, 9% strand | P04141 |
| H | Immunglobulin G1 Fab fragment, heavy chain | protein | 211 | 6% helix, 51% strand | — |
| L | Immunglobulin G1 Fab fragment, light chain | protein | 198 | 9% helix, 52% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 368 | 0.55 | 0.74 | 44 | empty |
| 2 | 222 | 0.48 | 0.74 | 29 | empty |
| 3 | 207 | 0.44 | 0.73 | 26 | empty |
| 4 | 94 | 0.41 | 0.78 | 19 | empty |
| 5 | 70 | 0.31 | 0.74 | 13 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1596 Ų buried · 15 hydrogen bonds · protein-protein
- A–H · 488 Ų buried · 4 hydrogen bonds · protein-protein
- A–L · 433 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5D71 · Crystal structure of MOR04302, a neutralizing anti-human GM-CSF antibody Fab fragment in… · the same entry in another collection · chain A against A, TM-score 1.00
- P04141 · AlphaFold monomer V2.0 prediction for granulocyte-macrophage colony- stimulating factor… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P04141
- Elsewhere: RCSB PDB 5D71 · PDBe 5D71 · UniProt P04141
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