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Crystal structure of the murine class I major histocompatibility complex H-2DB in complex with the lcmv-derived GP33 altered peptide ligand (V3P, Y4F)

Analyse Crystal structure of the murine class I major histocompatibility complex H-2DB… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3TBY
Type: protein
Length: 1,490 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 0.71

Structure

x-ray diffraction · 5 distinct chains · 22% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	H-2 class I histocompatibility antigen, D-B alpha chain	protein	266	25% helix, 38% strand	P01899
B, E, H, K	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P01887
C, F, I, L	Glycoprotein gpc	protein	9	0% helix, 0% strand	P07399
G	H-2 class I histocompatibility antigen, D-B alpha chain	protein	264	26% helix, 38% strand	P01899
J	H-2 class I histocompatibility antigen, D-B alpha chain	protein	262	26% helix, 38% strand	P01899

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1172	0.71	0.75	101	empty
2	377	0.65	0.79	44	empty
3	426	0.64	0.77	59	empty
4	401	0.63	0.78	46	empty
5	373	0.63	0.78	44	empty

Interfaces

15 interfaces between chains.

A–B · 1287 Å² buried · 21 hydrogen bonds · protein-protein
G–H · 1285 Å² buried · 21 hydrogen bonds · protein-protein
D–E · 1271 Å² buried · 24 hydrogen bonds · protein-protein
J–K · 1233 Å² buried · 18 hydrogen bonds · protein-protein
J–L · 931 Å² buried · 24 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

3TBY · CRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX H-2DB IN COMPLEX… · 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 3TBY · PDBe 3TBY · UniProt P01899 · UniProt P01887 · UniProt P07399

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