MolNFT v1 · #82320 · protein

Structure of the MHC class ib molecule qa-1B

3VJ6 · H-2 class I histocompatibility antigen, D-37 alpha chain: “Structure of the MHC class ib molecule qa-1B”. X-ray diffraction, 1 ligand (NI), 6 pockets (best druggability 0.54). MolNFT v1 #82320 on GenesisL1: 3D structure, binding…

PDB: 3VJ6
Type: protein
Length: 386 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H-2 class I histocompatibility antigen, D-37 alpha chain; Beta-2-microglobulin; Qdm…
UniProt: P06339, P01887, P01897
Ligands: NI
Pockets: 6 · best druggability 0.54

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H-2 class I histocompatibility antigen, D-37 alpha chain	protein	277	27% helix, 39% strand	P06339
B	Beta-2-microglobulin	protein	100	0% helix, 52% strand	P01887
P	Qdm peptide	protein	9	0% helix, 0% strand	P01897

Ligands and binding sites

NI · Nickel (II) ion · metal · 4 copies · chains A, B

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	187	0.54	0.78	20	empty
2	164	0.49	0.78	25	empty
3	165	0.48	0.76	33	empty
4	63	0.38	0.79	17	empty
5	93	0.33	0.73	20	empty

Interfaces

2 interfaces between chains.

A–B · 1383 Å² buried · 18 hydrogen bonds · protein-protein
A–P · 902 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

3VJ6 · Structure of the MHC class Ib molecule Qa-1b · the same entry in another collection · chain A against A, TM-score 1.00
P06339 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, D-37 alpha… · a predicted model of the same protein · chain A against A, TM-score 0.98
P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B against A, TM-score 0.98
P01897 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, L-D alpha… · a predicted model of the same protein · chain P against A, TM-score 0.31

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 P06339
Every structure of UniProt P01887
Every structure of UniProt P01897
Elsewhere: RCSB PDB 3VJ6 · PDBe 3VJ6 · UniProt P06339 · UniProt P01887 · UniProt P01897

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