Research workbench

Fab structure of CD4 binding site (CD4BS) huamn monoclonal antibody HMAB64

Analyse Fab structure of CD4 binding site (CD4BS) huamn monoclonal antibody HMAB64 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6W73
Type: protein
Length: 435 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HMAB64 Fab light chain; HMAB64 Fab heavy chain
Ligands: CA
Pockets: 3 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	HMAB64 Fab light chain	protein	211	6% helix, 51% strand	—
H	HMAB64 Fab heavy chain	protein	224	7% helix, 52% strand	—

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains L

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

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	600	0.63	0.74	61	empty
2	91	0.34	0.74	18	empty
3	52	0.27	0.74	17	empty

Interfaces

1 interface between chains.

L–H · 1970 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6W73 · Fab Structure of CD4 Binding Site (CD4bs) Huamn Monoclonal Antibody HmAb64 · 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 6W73 · PDBe 6W73

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