Research workbench

Crystal structure of B*27:04 complex bound to the pvipr peptide

Analyse Crystal structure of B*27:04 complex bound to the pvipr peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5DEF
Type: protein
Length: 385 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, B-27 alpha chain; Beta-2-microglobulin; Peptide…
UniProt: U6BN38, P61769
Ligands: CL
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	HLA class I histocompatibility antigen, B-27 alpha chain	protein	276	26% helix, 39% strand	U6BN38
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C	Peptide derived from vasoactive intestinal polypeptide receptor 1 (pvipr)	protein	9	0% helix, 0% strand	—

Ligands and binding sites

CL · Chloride ion · ion · chains A, C
GOL · Glycerol · additive · 4 copies · chains A, C, B

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	656	0.70	0.78	53	GOL
2	134	0.50	0.80	21	empty
3	78	0.41	0.79	15	empty
4	59	0.41	0.81	16	GOL

Interfaces

2 interfaces between chains.

A–B · 1352 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 1125 Å² buried · 24 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5DEF · Crystal structure of B*27:04 complex bound to the pVIPR peptide · the same entry in another collection · chain B against B, 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 U6BN38
Every structure of UniProt P61769
Elsewhere: RCSB PDB 5DEF · PDBe 5DEF · UniProt U6BN38 · UniProt P61769

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