MolNFT v1 · #136805 · protein

Engineered human IgG Fc domain GLYCO801 (FC801)

5V4E · Ig gamma-1 chain C region: “Engineered human IgG Fc domain GLYCO801 (FC801)”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 11 pockets (best druggability 0.70). MolNFT v1 #136805 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5V4E
Type: protein
Length: 1,586 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ig gamma-1 chain C region
UniProt: P01857
Ligands: NAG, MAN, BMA, FUC, K
Pockets: 11 · best druggability 0.70

Structure

x-ray diffraction · 8 distinct chains · 11% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ig gamma-1 chain C region	protein	218	10% helix, 46% strand	P01857
B	Ig gamma-1 chain C region	protein	186	12% helix, 47% strand	P01857
C	Ig gamma-1 chain C region	protein	162	14% helix, 40% strand	P01857
D	Ig gamma-1 chain C region	protein	200	12% helix, 48% strand	P01857
E	Ig gamma-1 chain C region	protein	208	10% helix, 49% strand	P01857
F	Ig gamma-1 chain C region	protein	177	8% helix, 45% strand	P01857
G	Ig gamma-1 chain C region	protein	219	10% helix, 46% strand	P01857
H	Ig gamma-1 chain C region	protein	216	11% helix, 49% strand	P01857

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, C, D, E, G, H, B
MAN · alpha-D-mannopyranose · sugar · 12 copies · chains A, D, E, G, H, B
BMA · beta-D-mannopyranose · sugar · 6 copies · chains A, C, D, E, G, H
FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, E, G, H
K · Potassium ion · metal · 2 copies · chains A, D, G

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	557	0.70	0.79	70	K
2	591	0.66	0.76	58	empty
3	190	0.59	0.82	31	empty
4	225	0.58	0.80	41	empty
5	161	0.52	0.79	38	empty

Interfaces

11 interfaces between chains.

G–H · 1430 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 1129 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 1120 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 1052 Å² buried · 6 hydrogen bonds · protein-protein
D–G · 803 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

5V4E · Engineered human IgG Fc domain glyco801 (Fc801) · the same entry in another collection · chain A against A, 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
Every structure of UniProt P01857
Elsewhere: RCSB PDB 5V4E · PDBe 5V4E · UniProt P01857

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