MolNFT v1 · #155640 · protein

Structure antibody E6 in complex with methylated peptide

6LDX · Fab heavy chain: “Structure antibody E6 in complex with methylated peptide”. X-ray diffraction, 1 ligand (CL), 4 pockets (best druggability 0.60). MolNFT v1 #155640 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6LDX
Type: protein
Length: 435 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab heavy chain; Fab light chain; Gly-M3L-gly-gly-thr-tyr-pro
Ligands: CL
Pockets: 4 · best druggability 0.60

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab heavy chain	protein	214	4% helix, 51% strand	—
L	Fab light chain	protein	214	9% helix, 53% strand	—
B	Gly-M3L-gly-gly-thr-tyr-pro	protein	7	0% helix, 0% strand	—

Ligands and binding sites

CL · Chloride ion · ion · chains H, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	478	0.60	0.74	56	empty
2	64	0.46	0.83	21	empty
3	79	0.37	0.77	23	empty
4	85	0.35	0.75	17	empty

Interfaces

3 interfaces between chains.

H–L · 1828 Å² buried · 17 hydrogen bonds · protein-protein
H–B · 533 Å² buried · 11 hydrogen bonds · protein-protein
L–B · 216 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 1 modified (disulfide, methylation).

Compared structures

6LDX · Structure antibody E6 in complex with methylated peptide · 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 6LDX · PDBe 6LDX

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