MolNFT v1 · #76761 · protein

Crystal structures of the murine class I major histocompatibility complex H-2DB in complex with lcmv-derived GP33 altered peptide ligand (Y4S)

3QUL · H-2 class I histocompatibility antigen, D-B alpha chain: “Crystal structures of the murine class I major histocompatibility complex H-2DB in complex with lcmv-derived…”. X-ray diffraction, 20 pockets (best druggability 0.72). MolNFT…

PDB: 3QUL
Type: protein
Length: 1,495 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H-2 class I histocompatibility antigen, D-B alpha chain; Beta-2-microglobulin…
UniProt: P01899, P01887, P07399
Pockets: 20 · best druggability 0.72

Structure

x-ray diffraction · 6 distinct chains · 24% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H-2 class I histocompatibility antigen, D-B alpha chain	protein	264	28% helix, 38% strand	P01899
B, E, H, K	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P01887
C, F, I, L	Pre-glycoprotein polyprotein gp complex	protein	9	0% helix, 0% strand	P07399
D	H-2 class I histocompatibility antigen, D-B alpha chain	protein	262	26% helix, 39% strand	P01899
G	H-2 class I histocompatibility antigen, D-B alpha chain	protein	270	26% helix, 39% strand	P01899
J	H-2 class I histocompatibility antigen, D-B alpha chain	protein	267	26% helix, 39% strand	P01899

Pockets

20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	757	0.72	0.78	61	empty
2	950	0.71	0.75	72	empty
3	568	0.64	0.76	45	empty
4	445	0.64	0.77	42	empty
5	350	0.59	0.76	40	empty

Interfaces

16 interfaces between chains.

G–H · 1335 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1287 Å² buried · 23 hydrogen bonds · protein-protein
J–K · 1286 Å² buried · 24 hydrogen bonds · protein-protein
D–E · 1243 Å² buried · 17 hydrogen bonds · protein-protein
D–F · 904 Å² buried · 27 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

3QUL · Crystal structures of the murine class I major histocompatibility complex H-2Db in… · the same entry in another collection · chain L against L, TM-score 1.00

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 P01899
Every structure of UniProt P01887
Every structure of UniProt P07399
Elsewhere: RCSB PDB 3QUL · PDBe 3QUL · UniProt P01899 · UniProt P01887 · UniProt P07399

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.