MolNFT v1 · #153773 · protein

Human antibody 32D6 Fab in complex with peg

6JP7 · Immunoglobulin Fab heavy chain: “Human antibody 32D6 Fab in complex with peg”. X-ray diffraction, 1 ligand (3FX), 7 pockets (best druggability 0.46). MolNFT v1 #153773 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6JP7
Type: protein
Length: 454 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Immunoglobulin Fab heavy chain; Immunoglobulin Fab light chain
Ligands: 3FX
Pockets: 7 · best druggability 0.46

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Immunoglobulin Fab heavy chain	protein	238	10% helix, 49% strand	—
L	Immunoglobulin Fab light chain	protein	216	8% helix, 52% strand	—

Ligands and binding sites

3FX · (2R)-3-(cyclohexylamino)-2-hydroxypropane-1-sulfonic acid · ligand · 2 copies · chains H, L
P6G · Hexaethylene glycol · additive · 2 copies · chains H, L

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

Pockets

7 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	245	0.46	0.73	41	3FX, P6G
2	119	0.46	0.79	22	empty
3	76	0.46	0.82	22	empty
4	115	0.41	0.76	21	empty
5	88	0.33	0.74	17	3FX

Interfaces

1 interface between chains.

H–L · 1988 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

6JP7 · Human antibody 32D6 Fab in complex with PEG · 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 6JP7 · PDBe 6JP7

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