Research workbench

Fv IgE spe-7 in complex with alizarin red

Analyse Fv IgE spe-7 in complex with alizarin red in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1OAR
Type: protein
Length: 839 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Immunoglobulin E; Immunoglobuling E
Ligands: AZN, NA, CL
Pockets: 8 · best druggability 0.59

Structure

x-ray diffraction · 6 distinct chains · 4% helix, 55% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H, J	Immunoglobulin E	protein	122	7% helix, 53% strand	—
I	Immunoglobulin E	protein	88	0% helix, 53% strand	—
K	Immunoglobulin E	protein	82	0% helix, 55% strand	—
L, N	Immunoglobuling E	protein	108	6% helix, 57% strand	—
M	Immunoglobuling E	protein	103	6% helix, 55% strand	—
O	Immunoglobuling E	protein	106	6% helix, 58% strand	—

Ligands and binding sites

AZN · Alizarin red · ligand · 4 copies · chains H, L, O, I, M, J, N, K
NA · Sodium ion · metal · 6 copies · chains L, N, J, M
CL · Chloride ion · ion · 8 copies · chains J, H, L, M, N, O
DMS · Dimethyl sulfoxide · additive · 24 copies · chains H, O, J, M, L, N
CAC · Cacodylate ion · additive · 2 copies · chains H, L, J, N
EDO · 1,2-ethanediol · additive · 2 copies

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

Pockets

8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	217	0.59	0.80	41	DMS, AZN
2	138	0.54	0.81	26	AZN
3	50	0.44	0.83	15	AZN
4	156	0.43	0.75	28	DMS, CL
5	95	0.41	0.77	20	empty

Interfaces

9 interfaces between chains.

J–N · 884 Å² buried · 8 hydrogen bonds · protein-protein
H–L · 875 Å² buried · 7 hydrogen bonds · protein-protein
K–O · 853 Å² buried · 7 hydrogen bonds · protein-protein
I–M · 848 Å² buried · 7 hydrogen bonds · protein-protein
H–O · 245 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

1OAR · Fv IgE SPE-7 in complex with Alizarin Red · the same entry in another collection · chain N against N, 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 1OAR · PDBe 1OAR

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