MolNFT v1 · #104021 · protein

Crystal structure of Fab 3.1

4PY7 · Antibody 3.1 heavy chain: “Crystal structure of Fab 3.1”. X-ray diffraction, 8 pockets (best druggability 0.68). MolNFT v1 #104021 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4PY7
Type: protein
Length: 855 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antibody 3.1 heavy chain; Antibody 3.1 light chain
Pockets: 8 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
I	Antibody 3.1 heavy chain	protein	215	8% helix, 51% strand	—
J, B	Antibody 3.1 light chain	protein	212	6% helix, 50% strand	—
A	Antibody 3.1 heavy chain	protein	216	7% helix, 50% strand	—

Pockets

8 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	716	0.68	0.76	75	empty
2	266	0.52	0.75	38	empty
3	237	0.50	0.75	31	empty
4	93	0.38	0.76	22	empty
5	97	0.36	0.75	21	empty

Interfaces

3 interfaces between chains.

I–J · 1666 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 1646 Å² buried · 11 hydrogen bonds · protein-protein
J–A · 818 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

4PY7 · Crystal Structure of Fab 3.1 · the same entry in another collection · chain I against I, 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 4PY7 · PDBe 4PY7

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