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Crystal structure of H-2DB in complex with the lcmv-derived GP92-101 peptide

Analyse Crystal structure of H-2DB in complex with the lcmv-derived GP92-101 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5JWE
Type: protein
Length: 1,529 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, P09991
Ligands: SO4
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 5 distinct chains · 23% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	H-2 class I histocompatibility antigen, D-B alpha chain	protein	276	27% helix, 40% strand	P01899
B, D, F, H	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P01887
E	H-2 class I histocompatibility antigen, D-B alpha chain	protein	268	25% helix, 39% strand	P01899
G	H-2 class I histocompatibility antigen, D-B alpha chain	protein	273	26% helix, 40% strand	P01899
P, Q, R, S	Pre-glycoprotein polyprotein gp complex	protein	10	0% helix, 0% strand	P09991

Ligands and binding sites

SO4 · Sulfate ion · ion · 13 copies · chains A, B, D, F, E, G, H
GOL · Glycerol · additive · 15 copies · chains A, B, C, D, E, F, G, H

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

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	792	0.76	0.80	99	GOL
2	524	0.68	0.78	60	GOL
3	550	0.67	0.77	67	GOL
4	423	0.66	0.79	44	GOL
5	383	0.63	0.78	53	GOL

Interfaces

18 interfaces between chains.

G–H · 1329 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 1316 Å² buried · 23 hydrogen bonds · protein-protein
E–F · 1277 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1265 Å² buried · 20 hydrogen bonds · protein-protein
E–R · 853 Å² buried · 27 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

5JWE · Crystal structure of H-2Db in complex with the LCMV-derived GP92-101 peptide · the same entry in another collection · chain S against S, 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 P09991
Elsewhere: RCSB PDB 5JWE · PDBe 5JWE · UniProt P01899 · UniProt P01887 · UniProt P09991

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