MolNFT v1 · #14613 · protein

Antibody catalysis of a bimolecular cycloaddition reaction

1MEX · Fab 29G12 light chain: “Antibody catalysis of a bimolecular cycloaddition reaction”. X-ray diffraction, 1 ligand (RAC), 4 pockets (best druggability 0.67). MolNFT v1 #14613 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 1MEX
Type: protein
Length: 424 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab 29G12 light chain; Fab 29G12 heavy chain
Ligands: RAC
Pockets: 4 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Fab 29G12 light chain	protein	213	6% helix, 50% strand	—
H	Fab 29G12 heavy chain	protein	211	10% helix, 52% strand	—

Ligands and binding sites

RAC · 4-(2-dimethylcarbamoyl-phenylcarbamoyloxymethyl)-benzoic acid · ligand · chains L, H

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	153	0.67	0.87	19	RAC
2	371	0.58	0.76	50	empty
3	236	0.50	0.75	38	empty
4	69	0.49	0.84	22	empty

Interfaces

1 interface between chains.

L–H · 1606 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

1MEX · Antibody Catalysis of a Bimolecular Cycloaddition Reaction · the same entry in another collection · chain L against L, 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 1MEX · PDBe 1MEX

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