MolNFT v1 · #59687 · protein

Crystal structure of HLA DR52C

3C5J · HLA class II histocompatibility antigen, dr alpha chain: “Crystal structure of HLA DR52C”. X-ray diffraction, 2 ligands (NAG, SO4), 3 pockets (best druggability 0.40). MolNFT v1 #59687 on GenesisL1: 3D structure, binding sites and…

PDB: 3C5J
Type: protein
Length: 373 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class II histocompatibility antigen, dr alpha chain; MHC class II antigen; Elongation…
UniProt: P01903, Q6YJU6, Q05639
Ligands: NAG, SO4
Pockets: 3 · best druggability 0.40

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	MHC class II antigen	protein	182	19% helix, 46% strand	Q6YJU6
C	Elongation factor 1-alpha 2	protein	13	0% helix, 8% strand	Q05639

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
SO4 · Sulfate ion · ion · chains A, 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	119	0.40	0.76	16	empty
2	67	0.29	0.73	15	empty
3	57	0.27	0.73	20	empty

Interfaces

3 interfaces between chains.

A–B · 2376 Å² buried · 32 hydrogen bonds · protein-protein
A–C · 619 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 556 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

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

Compared structures

3C5J · Crystal structure of HLA DR52c · 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
Q05639 · AlphaFold monomer V2.0 prediction for elongation factor 1-alpha 2 (Q05639) · a predicted model of the same protein · chain C against A, TM-score 0.34

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 Q6YJU6
Every structure of UniProt Q05639
Elsewhere: RCSB PDB 3C5J · PDBe 3C5J · UniProt P01903 · UniProt Q6YJU6 · UniProt Q05639

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