MolNFT v1 · #12386 · protein

Crystal structure of Fab fragment complexed with gibberellin A4

1KFA · Monoclonal antibody light chain: “Crystal structure of Fab fragment complexed with gibberellin A4”. X-ray diffraction, 1 ligand (GA4), 11 pockets (best druggability 0.76). MolNFT v1 #12386 on GenesisL1: 3D structure, binding sites…

PDB: 1KFA
Type: protein
Length: 852 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Monoclonal antibody light chain; Monoclonal antibody heavy chain
Ligands: GA4
Pockets: 11 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 6% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Monoclonal antibody light chain	protein	217	6% helix, 51% strand	—
H	Monoclonal antibody heavy chain	protein	213	6% helix, 51% strand	—
M	Monoclonal antibody light chain	protein	213	6% helix, 48% strand	—
I	Monoclonal antibody heavy chain	protein	209	7% helix, 50% strand	—

Ligands and binding sites

GA4 · Gibberellin A4 · ligand · 2 copies · chains H, I

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

Pockets

11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	571	0.76	0.83	60	empty
2	229	0.65	0.84	37	empty
3	597	0.61	0.73	48	empty
4	398	0.56	0.74	46	empty
5	56	0.50	0.87	24	empty

Interfaces

6 interfaces between chains.

L–H · 1828 Å² buried · 19 hydrogen bonds · protein-protein
M–I · 1821 Å² buried · 16 hydrogen bonds · protein-protein
L–I · 256 Å² buried · 5 hydrogen bonds · protein-protein
H–M · 164 Å² buried · 2 hydrogen bonds · protein-protein
L–M · 52 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

1KFA · Crystal structure of Fab fragment complexed with gibberellin A4 · the same entry in another collection · chain M against M, 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 1KFA · PDBe 1KFA

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