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Crystal structure of HLA-G presenting klpaqfyil peptide

Analyse Crystal structure of HLA-G presenting klpaqfyil peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3KYO
Type: protein
Length: 764 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I antigen; Beta-2-microglobulin; Klpaqfyil peptide
UniProt: Q9MYA2, P61769
Ligands: CO
Pockets: 9 · best druggability 0.70

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	MHC class I antigen	protein	273	27% helix, 40% strand	Q9MYA2
B, D	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
P, Q	Klpaqfyil peptide	protein	9	0% helix, 0% strand	—

Ligands and binding sites

CO · Cobalt (II) ion · metal · 2 copies · chains B, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	696	0.70	0.77	52	empty
2	669	0.70	0.78	50	empty
3	154	0.54	0.80	24	empty
4	216	0.52	0.77	32	empty
5	150	0.52	0.79	27	empty

Interfaces

7 interfaces between chains.

A–B · 1350 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1336 Å² buried · 24 hydrogen bonds · protein-protein
A–P · 901 Å² buried · 15 hydrogen bonds · protein-protein
C–Q · 872 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 127 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

3KYO · Crystal structure of HLA-G presenting KLPAQFYIL peptide · the same entry in another collection · chain Q against Q, TM-score 1.00
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain D 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 Q9MYA2
Every structure of UniProt P61769
Elsewhere: RCSB PDB 3KYO · PDBe 3KYO · UniProt Q9MYA2 · UniProt P61769

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