MolNFT v1 · #6139 · protein

Histocompatibility antigen I-AG7

1F3J · H-2 class II histocompatibility antigen: “Histocompatibility antigen I-AG7”. X-ray diffraction, 1 ligand (NAG), 10 pockets (best druggability 0.75). MolNFT v1 #6139 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1F3J
Type: protein
Length: 766 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H-2 class II histocompatibility antigen; MHC class II nod; Lysozyme C
UniProt: P04228, Q31135, P00698
Ligands: NAG
Pockets: 10 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 13% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	H-2 class II histocompatibility antigen	protein	182	11% helix, 44% strand	P04228
B, E	MHC class II nod	protein	187	16% helix, 44% strand	Q31135
P, Q	Lysozyme C	protein	14	0% helix, 0% strand	P00698

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, D, E

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

Pockets

10 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	867	0.75	0.79	82	empty
2	504	0.68	0.79	51	empty
3	615	0.66	0.76	57	empty
4	66	0.44	0.81	16	empty
5	123	0.43	0.77	23	empty

Interfaces

9 interfaces between chains.

A–B · 2517 Å² buried · 42 hydrogen bonds · protein-protein
D–E · 2510 Å² buried · 43 hydrogen bonds · protein-protein
B–P · 809 Å² buried · 17 hydrogen bonds · protein-protein
E–Q · 808 Å² buried · 16 hydrogen bonds · protein-protein
A–P · 730 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 6 glycan (disulfide, N-glycosylation).

Compared structures

1F3J · Histocompatibility antigen I-AG7 · the same entry in another collection · chain P against P, TM-score 1.00
P04228 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, a-D alpha… · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P04228
Every structure of UniProt Q31135
Every structure of UniProt P00698
Elsewhere: RCSB PDB 1F3J · PDBe 1F3J · UniProt P04228 · UniProt Q31135 · UniProt P00698

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