Research workbench

Crystal structure of HLA-C*07:02 in complex with ryr peptide

Analyse Crystal structure of HLA-C*07:02 in complex with ryr peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5VGE
Type: protein
Length: 384 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cdna FLJ54183, highly similar to HLA class I histocompatibility antigen, cw-7 alpha…
UniProt: B4DVY0, P61769
Ligands: ZN
Pockets: 4 · best druggability 0.70

Structure

x-ray diffraction · 3 distinct chains · 18% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cdna FLJ54183, highly similar to HLA class I histocompatibility antigen, cw-7 alpha chain	protein	275	25% helix, 40% strand	B4DVY0
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C	Arg-tyr-arg-pro-gly-thr-val-ala-leu	protein	9	0% helix, 0% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 3 copies · chains A

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

Pockets

4 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	678	0.70	0.78	58	empty
2	119	0.47	0.79	21	empty
3	52	0.35	0.79	17	empty
4	69	0.35	0.77	16	empty

Interfaces

2 interfaces between chains.

A–B · 1350 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 933 Å² buried · 21 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

5VGE · Crystal structure of HLA-C*07:02 in complex with RYR peptide · 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 0.98

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 B4DVY0
Every structure of UniProt P61769
Elsewhere: RCSB PDB 5VGE · PDBe 5VGE · UniProt B4DVY0 · UniProt P61769

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