MolNFT v1 · #154509 · protein

Antibody 64M-5 Fab including isoasp in ligand-free form

6KDH · Anti-(6-4) photoproduct antibody 64M-5 Fab (light chain): “Antibody 64M-5 Fab including isoasp in ligand-free form”. X-ray diffraction, 5 pockets (best druggability 0.56). MolNFT v1 #154509 on GenesisL1: 3D structure, binding sites…

PDB: 6KDH
Type: protein
Length: 436 residues
Chains: 2
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: 5 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Anti-(6-4) photoproduct antibody 64M-5 Fab (light chain)	protein	218	6% helix, 51% strand	—
H	Anti-(6-4) photoproduct antibody 64M-5 Fab (heavy chain)	protein	218	7% helix, 53% strand	—

Pockets

5 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	397	0.56	0.74	55	empty
2	218	0.49	0.75	30	empty
3	78	0.33	0.74	19	empty
4	78	0.32	0.74	15	empty
5	71	0.28	0.73	18	empty

Interfaces

1 interface between chains.

L–H · 1857 Å² buried · 21 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6KDH · Antibody 64M-5 Fab including isoAsp in ligand-free form · 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 6KDH · PDBe 6KDH

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