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Crystal structure of a MR78-like antibody naive-1 Fab

Analyse Crystal structure of a MR78-like antibody naive-1 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6V4Q
Type: protein
Length: 434 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Naive-1 Fab heavy chain; Naive-1 Fab light chain
Pockets: 5 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Naive-1 Fab heavy chain	protein	222	10% helix, 53% strand	—
L	Naive-1 Fab light chain	protein	212	5% helix, 51% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 5 copies · chains H, L
IPA · Isopropyl alcohol · additive · chains L

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	234	0.56	0.78	37	empty
2	356	0.54	0.74	44	empty
3	56	0.51	0.87	22	GOL
4	93	0.37	0.75	19	GOL
5	70	0.31	0.74	17	empty

Interfaces

1 interface between chains.

H–L · 1970 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

6V4Q · Crystal structure of a MR78-like antibody naive-1 Fab · 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 6V4Q · PDBe 6V4Q

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