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Leptin receptor-antibody complex

Analyse Leptin receptor-antibody complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3V6O
Type: protein
Length: 1,224 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Leptin receptor; Monoclonal antibody 9F8 Fab fragment heavy chain; Monoclonal antibody…
UniProt: P48357
Ligands: CYS, NAG, NA
Pockets: 12 · best druggability 0.82

Structure

x-ray diffraction · 6 distinct chains · 5% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Leptin receptor	protein	181	2% helix, 44% strand	P48357
B	Leptin receptor	protein	184	2% helix, 45% strand	P48357
C	Monoclonal antibody 9F8 Fab fragment heavy chain	protein	219	8% helix, 51% strand	—
D	Monoclonal antibody 9F8 Fab fragment heavy chain	protein	215	6% helix, 53% strand	—
E	Monoclonal antibody 9F8 Fab fragment light chain	protein	213	7% helix, 51% strand	—
F	Monoclonal antibody 9F8 Fab fragment light chain	protein	212	6% helix, 51% strand	—

Ligands and binding sites

CYS · Cysteine · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains F
NA · Sodium ion · metal · chains C
EDO · 1,2-ethanediol · additive · 31 copies · chains A, B, F, D, E, C
ACT · Acetate ion · additive · 6 copies · chains A, B, C, D, E, F

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	932	0.82	0.84	100	EDO, ACT
2	1179	0.82	0.83	119	EDO, ACT
3	720	0.65	0.74	67	EDO
4	624	0.63	0.74	72	EDO
5	173	0.51	0.78	27	empty

Interfaces

11 interfaces between chains.

D–F · 1965 Å² buried · 20 hydrogen bonds · protein-protein
C–E · 1914 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 715 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 560 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 548 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 2 covalent, 1 glycan (disulfide, covalent ligand, N-glycosylation).

Compared structures

3V6O · Leptin Receptor-antibody complex · the same entry in another collection · chain F against F, TM-score 1.00
P48357 · AlphaFold monomer V2.0 prediction for leptin receptor (P48357) · a predicted model of the same protein · chain B 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 P48357
Elsewhere: RCSB PDB 3V6O · PDBe 3V6O · UniProt P48357

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