MolNFT v1 · #121890 · protein

HMM5 Fab in complex with disaccharide

5I8O · HMM5 antibody heavy chain: “HMM5 Fab in complex with disaccharide”. X-ray diffraction, 2 ligands (2F8, FUC), 3 pockets (best druggability 0.65). MolNFT v1 #121890 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5I8O
Type: protein
Length: 436 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HMM5 antibody heavy chain; HMM5 antibody light chain
Ligands: 2F8, FUC
Pockets: 3 · best druggability 0.65

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	HMM5 antibody heavy chain	protein	219	5% helix, 50% strand	—
L	HMM5 antibody light chain	protein	217	7% helix, 53% strand	—

Ligands and binding sites

2F8 · methyl 2-acetamido-2-deoxy-alpha-D-glucopyranoside · ligand · chains H, L
FUC · alpha-L-fucopyranose · sugar · chains H

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

Pockets

3 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	662	0.65	0.75	67	empty
2	154	0.54	0.80	33	empty
3	58	0.34	0.77	12	empty

Interfaces

1 interface between chains.

H–L · 1913 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

5I8O · HMM5 Fab in complex with disaccharide · 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 5I8O · PDBe 5I8O

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