MolNFT v1 · #99761 · protein

Immune receptor

4MD5 · HLA class II histocompatibility antigen, dr alpha chain: “Immune receptor”. X-ray diffraction, 2 ligands (CIR, NAG), 3 pockets (best druggability 0.44). MolNFT v1 #99761 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4MD5
Type: protein
Length: 382 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 histocompatibility…
UniProt: P01903, P13760, P08670
Ligands: CIR, NAG
Pockets: 3 · best druggability 0.44

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	180	14% helix, 47% strand	P01903
B	HLA class II histocompatibility antigen, DRB1-4 beta chain	protein	190	19% helix, 45% strand	P13760
C	Citrullinated vimentin	protein	12	0% helix, 8% strand	P08670

Ligands and binding sites

CIR · Citrulline · ligand · chains A, B, C
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
PGE · Triethylene glycol · additive · chains B

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

Pockets

3 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	170	0.44	0.74	23	empty
2	139	0.43	0.76	23	EDO
3	54	0.38	0.80	13	CIR

Interfaces

3 interfaces between chains.

A–B · 2517 Å² buried · 43 hydrogen bonds · protein-protein
A–C · 575 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 558 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

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

Compared structures

4MD5 · Immune Receptor · 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 P13760
Every structure of UniProt P08670
Elsewhere: RCSB PDB 4MD5 · PDBe 4MD5 · UniProt P01903 · UniProt P13760 · UniProt P08670

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