Research workbench

Structure of DBNA(11) peptides bound to H-2DB MHC-I

Analyse Structure of DBNA(11) peptides bound to H-2DB MHC-I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6X00
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-B alpha chain; Beta-2-microglobulin; Epitope…
EC: 3.2.1.18
UniProt: P01899, P61769, P03468
Ligands: SO4
Pockets: 3 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H-2 class I histocompatibility antigen, D-B alpha chain	protein	274	27% helix, 40% strand	P01899
B	Beta-2-microglobulin	protein	97	0% helix, 48% strand	P61769
C	Epitope from neuraminidase protein (na-181-191) (EC 3.2.1.18)	protein	11	0% helix, 0% strand	P03468

Ligands and binding sites

SO4 · Sulfate ion · ion · chains B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	687	0.69	0.76	58	empty
2	88	0.46	0.80	17	empty
3	107	0.40	0.76	28	empty

Interfaces

2 interfaces between chains.

A–B · 1245 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 817 Å² buried · 26 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

6X00 · Structure of DbNA(11) peptides bound to H-2Db MHC-I · the same entry in another collection · chain A against A, TM-score 1.00
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P61769
Every structure of UniProt P03468
Elsewhere: RCSB PDB 6X00 · PDBe 6X00 · UniProt P01899 · UniProt P61769 · UniProt P03468

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