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Crystal structure of H-2DB Y159F in complex with chimeric GP100

Analyse Crystal structure of H-2DB Y159F in complex with chimeric GP100 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4IHO
Type: protein
Length: 758 residues
Chains: 6
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; Nonameric…
UniProt: P01899, P01887
Ligands: SO4
Pockets: 9 · best druggability 0.69

Structure

x-ray diffraction · 5 distinct chains · 18% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H-2 class I histocompatibility antigen, D-B alpha chain	protein	272	26% helix, 38% strand	P01899
B	Beta-2-microglobulin	protein	97	0% helix, 48% strand	P01887
C, F	Nonameric peptide chimeric GP100	protein	9	0% helix, 0% strand	—
D	H-2 class I histocompatibility antigen, D-B alpha chain	protein	272	25% helix, 38% strand	P01899
E	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P01887

Ligands and binding sites

SO4 · Sulfate ion · ion · chains A
GOL · Glycerol · additive · 3 copies · chains A, B

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

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	794	0.69	0.76	58	empty
2	746	0.68	0.76	62	empty
3	313	0.55	0.75	34	empty
4	74	0.45	0.82	19	empty
5	100	0.41	0.77	17	empty

Interfaces

7 interfaces between chains.

D–E · 1315 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1251 Å² buried · 19 hydrogen bonds · protein-protein
D–F · 973 Å² buried · 27 hydrogen bonds · protein-protein
A–C · 972 Å² buried · 26 hydrogen bonds · protein-protein
B–D · 78 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

4IHO · Crystal structure of H-2Db Y159F in complex with chimeric gp100 · the same entry in another collection · chain F against F, TM-score 1.00
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

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
Elsewhere: RCSB PDB 4IHO · PDBe 4IHO · UniProt P01899 · UniProt P01887

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