MolNFT v1 · #62128 · protein

MHC class I H-2DD heavy chain complexed with beta-2 microglobulin and a variant peptide, PA9, from the human immunodeficiency virus (bal) envelope glycoprotein 120

3E6F · H-2 class I histocompatibility antigen, D-D alpha chain: “MHC class I H-2DD heavy chain complexed with beta-2 microglobulin and a variant peptide, PA9, from the human…”. X-ray diffraction, 4 pockets (best druggability 0.68). MolNFT…

PDB: 3E6F
Type: protein
Length: 381 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H-2 class I histocompatibility antigen, D-D alpha chain; Beta-2 microglobulin; Envelope…
UniProt: P01900, Q91XJ8, Q9YZ87
Pockets: 4 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H-2 class I histocompatibility antigen, D-D alpha chain	protein	273	26% helix, 41% strand	P01900
B	Beta-2 microglobulin	protein	99	0% helix, 49% strand	Q91XJ8
P	Envelope glycoprotein 9-residue peptide	protein	9	0% helix, 0% strand	Q9YZ87

Pockets

4 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	570	0.68	0.78	54	empty
2	76	0.52	0.85	18	empty
3	148	0.50	0.79	24	empty
4	50	0.30	0.76	13	empty

Interfaces

2 interfaces between chains.

A–B · 1336 Å² buried · 17 hydrogen bonds · protein-protein
A–P · 850 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

3E6F · MHC CLASS I H-2Dd Heavy chain complexed with Beta-2 Microglobulin and a variant peptide… · the same entry in another collection · chain A against A, TM-score 1.00
P01900 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, D-D alpha… · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P01900
Every structure of UniProt Q91XJ8
Every structure of UniProt Q9YZ87
Elsewhere: RCSB PDB 3E6F · PDBe 3E6F · UniProt P01900 · UniProt Q91XJ8 · UniProt Q9YZ87

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