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Crystal structure of H-2DB in complex with jhmv epitope S510

Analyse Crystal structure of H-2DB in complex with jhmv epitope S510 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2ZOK
Type: protein
Length: 1,458 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; 9-meric…
UniProt: P01899, P01887, Q02385
Ligands: SO4
Pockets: 16 · best druggability 0.76

Structure

x-ray diffraction · 6 distinct chains · 25% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H-2 class I histocompatibility antigen, D-B alpha chain	protein	252	28% helix, 36% strand	P01899
B, D, F, H	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P01887
C	H-2 class I histocompatibility antigen, D-B alpha chain	protein	258	26% helix, 40% strand	P01899
E	H-2 class I histocompatibility antigen, D-B alpha chain	protein	253	28% helix, 36% strand	P01899
G	H-2 class I histocompatibility antigen, D-B alpha chain	protein	263	27% helix, 38% strand	P01899
I, L, J, K	9-meric peptide from spike glycoprotein	protein	9	0% helix, 0% strand	Q02385

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, E, G, H, L, I
GOL · Glycerol · additive · 4 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

16 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	730	0.76	0.81	92	SO4
2	800	0.75	0.80	98	SO4
3	898	0.70	0.75	82	GOL
4	651	0.67	0.76	61	GOL
5	359	0.66	0.80	59	GOL

Interfaces

19 interfaces between chains.

E–F · 1305 Å² buried · 21 hydrogen bonds · protein-protein
G–H · 1244 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1242 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1235 Å² buried · 22 hydrogen bonds · protein-protein
A–I · 902 Å² buried · 24 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 11 disulfide, 4 modified (disulfide, nonstandard).

Compared structures

2ZOK · Crystal structure of H-2Db in complex with JHMV epitope S510 · the same entry in another collection · chain K against K, 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 Q02385
Elsewhere: RCSB PDB 2ZOK · PDBe 2ZOK · UniProt P01899 · UniProt P01887 · UniProt Q02385

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