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Structure of IGG1 Fab fragment in complex with biotincytidinamide

Analyse Structure of IGG1 Fab fragment in complex with biotincytidinamide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4S1D
Type: protein
Length: 1,702 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mab M33 Fab fragment, heavy chain; Mab M33 Fab fragment, light chain
Ligands: 41M, SO4
Pockets: 19 · best druggability 0.76

Structure

x-ray diffraction · 7 distinct chains · 5% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Mab M33 Fab fragment, heavy chain	protein	216	6% helix, 54% strand	—
L, F	Mab M33 Fab fragment, light chain	protein	213	6% helix, 54% strand	—
C	Mab M33 Fab fragment, heavy chain	protein	212	6% helix, 55% strand	—
D	Mab M33 Fab fragment, light chain	protein	211	7% helix, 50% strand	—
E	Mab M33 Fab fragment, heavy chain	protein	214	4% helix, 53% strand	—
O	Mab M33 Fab fragment, heavy chain	protein	213	3% helix, 55% strand	—
P	Mab M33 Fab fragment, light chain	protein	210	6% helix, 50% strand	—

Ligands and binding sites

41M · N~6~-{5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}-L-lysinamide · ligand · 4 copies · chains H, L, C, D, E, F, O, P
SO4 · Sulfate ion · ion · chains H, O

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

Pockets

19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	713	0.76	0.81	45	41M
2	800	0.68	0.75	67	empty
3	682	0.66	0.75	58	empty
4	633	0.65	0.75	56	empty
5	465	0.63	0.76	53	41M, SO4

Interfaces

11 interfaces between chains.

H–L · 1951 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 1874 Å² buried · 17 hydrogen bonds · protein-protein
E–F · 1837 Å² buried · 12 hydrogen bonds · protein-protein
O–P · 1784 Å² buried · 13 hydrogen bonds · protein-protein
F–O · 401 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

4S1D · Structure of IgG1 Fab fragment in complex with Biotincytidinamide · the same entry in another collection · chain H against H, 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 4S1D · PDBe 4S1D

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