MolNFT v1 · #191015 · protein

OMI-12 FAB

7ZF6 · Omi-12 heavy chain: “OMI-12 FAB”. X-ray diffraction, 2 ligands (NAG, SO4), 2 pockets (best druggability 0.67). MolNFT v1 #191015 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7ZF6
Type: protein
Length: 436 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Omi-12 heavy chain; Omi-12 light chain
Ligands: NAG, SO4
Pockets: 2 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Omi-12 heavy chain	protein	224	7% helix, 50% strand	—
L	Omi-12 light chain	protein	212	8% helix, 52% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
SO4 · Sulfate ion · ion · 10 copies · chains H, L
GOL · Glycerol · additive · 3 copies · chains H, L
CIT · Citric acid · additive · chains H, L

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

Pockets

2 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	777	0.67	0.75	63	empty
2	57	0.27	0.73	19	empty

Interfaces

1 interface between chains.

H–L · 1942 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

7ZF6 · Omi-12 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 7ZF6 · PDBe 7ZF6

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