MolNFT v1 · #71357 · protein

Crystal structure of chimeric antibody X836

3MBX · X836 light chain: “Crystal structure of chimeric antibody X836”. X-ray diffraction, 2 ligands (NA, PO4), 5 pockets (best druggability 0.59). MolNFT v1 #71357 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3MBX
Type: protein
Length: 450 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: X836 light chain; X836 heavy chain
Ligands: NA, PO4
Pockets: 5 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	X836 light chain	protein	220	6% helix, 52% strand	—
H	X836 heavy chain	protein	230	8% helix, 49% strand	—

Ligands and binding sites

NA · Sodium ion · metal · chains L
PO4 · Phosphate ion · ion · chains H

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

Pockets

5 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	485	0.59	0.74	54	empty
2	145	0.59	0.83	25	empty
3	166	0.42	0.74	22	empty
4	85	0.36	0.76	22	empty
5	52	0.28	0.74	15	empty

Interfaces

1 interface between chains.

L–H · 2032 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide, 1 modified (disulfide, cyclization).

Compared structures

3MBX · Crystal structure of chimeric antibody X836 · 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 3MBX · PDBe 3MBX

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