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Crystal structure of H2-dd with disulfide-linked 10MER peptide

Analyse Crystal structure of H2-dd with disulfide-linked 10MER peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5WEU
Type: protein
Length: 382 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H-2 class I histocompatibility antigen, D-D alpha chain; Beta-2-microglobulin; Envelope…
UniProt: P01900, P01887, P03377
Pockets: 6 · best druggability 0.70

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H-2 class I histocompatibility antigen, D-D alpha chain	protein	273	26% helix, 38% strand	P01900
B	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P01887
P	Envelope glycoprotein GP160	protein	10	0% helix, 0% strand	P03377

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 6 copies · chains A, P, B

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	656	0.70	0.78	55	empty
2	200	0.54	0.78	32	EDO
3	86	0.43	0.79	23	EDO
4	52	0.35	0.79	15	empty
5	54	0.29	0.75	16	EDO

Interfaces

2 interfaces between chains.

A–B · 1242 Å² buried · 21 hydrogen bonds · protein-protein
A–P · 902 Å² buried · 24 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5WEU · Crystal Structure of H2-Dd with disulfide-linked 10mer peptide · the same entry in another collection · chain A against A, 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
P01900 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, D-D alpha… · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P01900
Every structure of UniProt P01887
Every structure of UniProt P03377
Elsewhere: RCSB PDB 5WEU · PDBe 5WEU · UniProt P01900 · UniProt P01887 · UniProt P03377

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