MolNFT v1 · #103071 · protein

MHC TCR peptide complex

4P57 · HLA class II histocompatibility antigen, dp alpha 1 chain: “MHC TCR peptide complex”. X-ray diffraction, 2 ligands (NAG, CA), 6 pockets (best druggability 0.59). MolNFT v1 #103071 on GenesisL1: 3D structure, binding sites and…

PDB: 4P57
Type: protein
Length: 751 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class II histocompatibility antigen, dp alpha 1 chain; MIM2 PEPTIDE,HLA class II…
UniProt: P20036, Q5EP54
Ligands: NAG, CA
Pockets: 6 · best druggability 0.59

Structure

x-ray diffraction · 4 distinct chains · 15% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class II histocompatibility antigen, dp alpha 1 chain	protein	178	15% helix, 45% strand	P20036
B	MIM2 PEPTIDE,HLA class II histocompatibility antigen, dp beta 1 chain	protein	197	15% helix, 44% strand	Q5EP54
C	HLA class II histocompatibility antigen, dp alpha 1 chain	protein	180	14% helix, 46% strand	P20036
D	MIM2 PEPTIDE,HLA class II histocompatibility antigen, dp beta 1 chain	protein	196	15% helix, 44% strand	Q5EP54

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B, C, D
CA · Calcium ion · metal · 2 copies · chains B, D
GOL · Glycerol · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	452	0.59	0.75	47	empty
2	154	0.43	0.75	26	empty
3	160	0.41	0.73	28	empty
4	114	0.39	0.75	20	empty
5	80	0.30	0.73	21	empty

Interfaces

4 interfaces between chains.

C–D · 3166 Å² buried · 62 hydrogen bonds · protein-protein
A–B · 3157 Å² buried · 61 hydrogen bonds · protein-protein
B–C · 191 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 83 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 5 glycan (disulfide, N-glycosylation).

Compared structures

4P57 · MHC TCR peptide complex · the same entry in another collection · chain A against A, TM-score 1.00
P20036 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dp alpha 1… · a predicted model of the same protein · chain C 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 P20036
Every structure of UniProt Q5EP54
Elsewhere: RCSB PDB 4P57 · PDBe 4P57 · UniProt P20036 · UniProt Q5EP54

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