MolNFT v1 · #27283 · protein

Structure of ligand-free Fab DNA-1 in space group P321 solved from crystals with perfect hemihedral twinning

1XF4 · Fab light chain: “Structure of ligand-free Fab DNA-1 in space group P321 solved from crystals with perfect hemihedral twinning”. X-ray diffraction, 1 ligand (SO4), 7 pockets (best druggability 0.60). MolNFT v1 #27283 on GenesisL1…

PDB: 1XF4
Type: protein
Length: 852 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab light chain; Fab heavy chain
Ligands: SO4
Pockets: 7 · best druggability 0.60

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, A	Fab light chain	protein	213	6% helix, 50% strand	—
H, B	Fab heavy chain	protein	213	8% helix, 53% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains L, A

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

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	483	0.60	0.75	67	empty
2	460	0.59	0.74	56	empty
3	89	0.32	0.73	25	empty
4	62	0.31	0.75	19	empty
5	55	0.29	0.75	16	empty

Interfaces

3 interfaces between chains.

A–B · 1688 Å² buried · 19 hydrogen bonds · protein-protein
L–H · 1663 Å² buried · 17 hydrogen bonds · protein-protein
H–B · 157 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

1XF4 · Structure of ligand-free Fab DNA-1 in space group P321 solved from crystals with perfect… · 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 1XF4 · PDBe 1XF4

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.