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64M-2 antibody Fab complexed with D(5HT)(6-4)T

Analyse 64M-2 antibody Fab complexed with D(5HT)(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: 1EHL
Type: protein + DNA
Length: 436 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-(D(5HT)P*(6-4)T)-3'; Anti-(6-4) photoproduct antibody 64M-2 Fab (light chain)…
Pockets: 3 · best druggability 0.49

Structure

x-ray diffraction · 3 distinct chains · 5% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5'-(D(5HT)P*(6-4)T)-3'	dna	2	—	—
L	Anti-(6-4) photoproduct antibody 64M-2 Fab (light chain)	protein	217	4% helix, 47% strand	—
H	Anti-(6-4) photoproduct antibody 64M-2 Fab (heavy chain)	protein	217	6% helix, 50% strand	—

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	250	0.49	0.74	42	empty
2	102	0.36	0.74	22	empty
3	74	0.30	0.73	17	empty

Interfaces

3 interfaces between chains.

L–H · 1804 Å² buried · 14 hydrogen bonds · protein-protein
A–H · 243 Å² buried · 4 hydrogen bonds · protein-nucleic
A–L · 166 Å² buried · 4 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 4 disulfide, 1 modified (disulfide, nucleotide modification).

Compared structures

1EHL · 64M-2 antibody Fab complexed with D(5HT)(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 1EHL · PDBe 1EHL

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