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Crystal structure of MOR03929, a neutralizing anti-human gm-csf antibody Fab fragment in complex with human gm-csf

Analyse Crystal structure of MOR03929, 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: 5D70
Type: protein
Length: 524 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: 5 · 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	115	50% helix, 9% strand	P04141
H	Immunglobulin G1 Fab fragment, heavy chain	protein	212	6% helix, 50% strand	—
L	Immunglobulin G1 Fab fragment, light chain	protein	197	8% helix, 52% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · chains L

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	359	0.55	0.74	42	empty
2	221	0.44	0.73	27	empty
3	96	0.42	0.78	20	empty
4	142	0.42	0.75	25	empty
5	98	0.36	0.74	17	SO4

Interfaces

3 interfaces between chains.

H–L · 1555 Å² buried · 12 hydrogen bonds · protein-protein
A–H · 478 Å² buried · 4 hydrogen bonds · protein-protein
A–L · 432 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

5D70 · Crystal structure of MOR03929, 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 0.95

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 5D70 · PDBe 5D70 · UniProt P04141

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