Research workbench

Antibody 64M-5 Fab in complex with DT(6-4)T

Analyse Antibody 64M-5 Fab in complex with DT(6-4)T in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6IDG
Type: protein + DNA
Length: 440 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Anti-(6-4) photoproduct antibody 64M-5 Fab (light chain); Anti-(6-4) photoproduct…
Pockets: 3 · best druggability 0.59

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Anti-(6-4) photoproduct antibody 64M-5 Fab (light chain)	protein	217	6% helix, 51% strand	—
H	Anti-(6-4) photoproduct antibody 64M-5 Fab (heavy chain)	protein	221	10% helix, 52% strand	—
A	DNA (5'-D((64T)P(5PY))-3')	dna	2	—	—

Pockets

3 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	542	0.59	0.73	58	empty
2	100	0.39	0.76	23	empty
3	63	0.36	0.78	14	empty

Interfaces

3 interfaces between chains.

L–H · 1845 Å² buried · 17 hydrogen bonds · protein-protein
H–A · 246 Å² buried · 5 hydrogen bonds · protein-nucleic
L–A · 163 Å² buried · 2 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 4 disulfide, 2 modified (disulfide, nucleotide modification).

Compared structures

6IDG · antibody 64M-5 Fab in complex with dT(6-4)T · 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 6IDG · PDBe 6IDG

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.