MolNFT v1 · #144088 · protein

HLA-DRB1 in complex with histone 2B peptide

6BIY · HLA class II histocompatibility antigen, dr alpha chain: “HLA-DRB1 in complex with histone 2B peptide”. X-ray diffraction, 1 ligand (NAG), 2 pockets (best druggability 0.41). MolNFT v1 #144088 on GenesisL1: 3D structure, binding…

PDB: 6BIY
Type: protein
Length: 380 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class II histocompatibility antigen, dr alpha chain; HLA class II dr-beta (HLA-dr B)…
UniProt: P01903, Q29890
Ligands: NAG
Pockets: 2 · best druggability 0.41

Structure

x-ray diffraction · 3 distinct chains · 16% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class II histocompatibility antigen, dr alpha chain	protein	178	15% helix, 47% strand	P01903
B	HLA class II dr-beta (HLA-dr B)	protein	189	19% helix, 45% strand	Q29890
C	HISTONE2B_69-81	protein	13	0% helix, 8% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains B

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	135	0.41	0.74	17	empty
2	100	0.39	0.76	16	empty

Interfaces

3 interfaces between chains.

A–B · 2405 Å² buried · 41 hydrogen bonds · protein-protein
B–C · 664 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 636 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

6BIY · HLA-DRB1 in complex with Histone 2B peptide · the same entry in another collection · chain A against A, TM-score 1.00
P01903 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dr alpha… · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P01903
Every structure of UniProt Q29890
Elsewhere: RCSB PDB 6BIY · PDBe 6BIY · UniProt P01903 · UniProt Q29890

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