MolNFT v1 · #102880 · protein

JR5.1 protein complex

4OZF · HLA class II histocompatibility antigen, dq alpha 1 chain: “JR5.1 protein complex”. X-ray diffraction, 1 ligand (NAG), 10 pockets (best druggability 0.73). MolNFT v1 #102880 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4OZF
Type: protein
Length: 810 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class II histocompatibility antigen, dq alpha 1 chain; HLA class II…
UniProt: P01909, Q5Y7D3
Ligands: NAG
Pockets: 10 · best druggability 0.73

Structure

x-ray diffraction · 5 distinct chains · 10% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class II histocompatibility antigen, dq alpha 1 chain	protein	181	14% helix, 45% strand	P01909
B	HLA class II histocompatibility antigen, dq beta 1 chain	protein	181	19% helix, 45% strand	Q5Y7D3
G	T-cell receptor, JR5.1 alpha chain	protein	193	3% helix, 44% strand	—
H	T-cell receptor, JR5.1 beta chain	protein	242	6% helix, 50% strand	—
J	Deamidated gliadin-ALPHA2 peptide	protein	13	0% helix, 0% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A

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	900	0.73	0.77	90	empty
2	122	0.59	0.85	28	empty
3	230	0.51	0.75	37	empty
4	224	0.50	0.76	38	empty
5	92	0.42	0.78	24	empty

Interfaces

10 interfaces between chains.

A–B · 2606 Å² buried · 52 hydrogen bonds · protein-protein
G–H · 2140 Å² buried · 25 hydrogen bonds · protein-protein
B–J · 682 Å² buried · 11 hydrogen bonds · protein-protein
A–J · 661 Å² buried · 11 hydrogen bonds · protein-protein
A–H · 363 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

4OZF · JR5.1 protein complex · the same entry in another collection · chain A against A, TM-score 1.00
P01909 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dq alpha 1… · 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 P01909
Every structure of UniProt Q5Y7D3
Elsewhere: RCSB PDB 4OZF · PDBe 4OZF · UniProt P01909 · UniProt Q5Y7D3

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