MolNFT v1 · #115045 · protein
Crystal structure of MOR04357, a neutralizing anti-human gm-csf antibody Fab fragment in complex with human gm-csf
5C7X · Granulocyte-macrophage colony-stimulating factor: “Crystal structure of MOR04357, a neutralizing anti-human gm-csf antibody Fab fragment in complex with human…”. X-ray diffraction, 12 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 5C7X
- Type
- protein
- Length
- 1,065 residues
- Chains
- 6
- 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
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 6 distinct chains · 17% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Granulocyte-macrophage colony-stimulating factor | protein | 115 | 54% helix, 9% strand | P04141 |
| B | Granulocyte-macrophage colony-stimulating factor | protein | 116 | 54% helix, 7% strand | P04141 |
| H | Immunglobulin G1 Fab fragment, heavy chain | protein | 214 | 7% helix, 49% strand | — |
| L | Immunglobulin G1 Fab fragment, light chain | protein | 206 | 7% helix, 48% strand | — |
| M | Immunglobulin G1 Fab fragment, heavy chain | protein | 213 | 6% helix, 48% strand | — |
| N | Immunglobulin G1 Fab fragment, light chain | protein | 201 | 7% helix, 50% strand | — |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains H, L, M, N
- PGE · Triethylene glycol · additive · 2 copies · chains A, H, L
- PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 734 | 0.72 | 0.78 | 72 | PGE |
| 2 | 509 | 0.59 | 0.74 | 58 | PEG |
| 3 | 242 | 0.54 | 0.76 | 30 | empty |
| 4 | 189 | 0.52 | 0.78 | 25 | empty |
| 5 | 360 | 0.52 | 0.73 | 40 | PEG |
Interfaces
9 interfaces between chains.
- H–L · 1573 Ų buried · 13 hydrogen bonds · protein-protein
- M–N · 1520 Ų buried · 14 hydrogen bonds · protein-protein
- A–L · 740 Ų buried · 8 hydrogen bonds · protein-protein
- B–N · 725 Ų buried · 9 hydrogen bonds · protein-protein
- A–H · 653 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5C7X · Crystal structure of MOR04357, a neutralizing anti-human GM-CSF antibody Fab fragment in… · the same entry in another collection · chain N against N, 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 0.97
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 5C7X · PDBe 5C7X · UniProt P04141
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