MolNFT v1 · #65980 · protein

Crystal structure of HLA-B*2709 complexed with the double citrullinated vasoactive intestinal peptide type 1 receptor (vipr) peptide (residues 400-408)

3HCV · HLA class I histocompatibility antigen, B-27 alpha chain: “Crystal structure of HLA-B*2709 complexed with the double citrullinated vasoactive intestinal peptide type 1…”. X-ray diffraction, 1 ligand (CIR), 5 pockets (best…

PDB: 3HCV
Type: protein
Length: 383 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; Double…
UniProt: P03989, P61769
Ligands: CIR
Pockets: 5 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class I histocompatibility antigen, B-27 alpha chain	protein	276	28% helix, 39% strand	P03989
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C	Double citrullinated vasoactive intestinal polypeptide receptor	protein	7	0% helix, 0% strand	—

Ligands and binding sites

CIR · Citrulline · ligand · 2 copies · chains A, C

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

Pockets

5 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	634	0.69	0.78	54	empty
2	100	0.60	0.87	17	CIR
3	128	0.49	0.79	18	empty
4	62	0.41	0.81	18	empty
5	80	0.39	0.78	16	empty

Interfaces

2 interfaces between chains.

A–B · 1391 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 974 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 2 covalent (disulfide, covalent ligand).

Compared structures

3HCV · Crystal structure of HLA-B*2709 complexed with the double citrullinated vasoactive… · 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 P03989
Every structure of UniProt P61769
Elsewhere: RCSB PDB 3HCV · PDBe 3HCV · UniProt P03989 · UniProt P61769

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